title: Soil sample 038 from Singapore

city: Shanghai

first: Lantian

last: Su

address: 800 Dongchuan Rd.

department: School of Agriculture and Biology

institute: Shanghai Jiaotong University

description: At each site, approximately 0.10 kg of soils was collected from surface (top 50 cm) for microbial Geochip analyses

hyb_protocol: 1.0 ug of Cy3-labelled DNA (specific activity >10.0 pmol Cy3/ug DNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Geochip 5.0 180k Microarrays (G4112A) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (GPL29739) using one color scan setting for 1x180k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The purified DNA was analyzed using GeoChip 5.0 (Glomics Inc.). The total of 1.0 μg DNA per each plot received labelling, hybridization and imaging as previously described35, and the raw signal intensity data was then preprocessed by a standard analysis pipeline (http://ieg.ou.edu/microarray).

organism: soil metagenome

source_name: Soil samples from urban park green space

label_protocol: Cyanine-3 (Cy3) labeled DNA was prepared from 1.0 ug DNA using the One-Color Low DNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by DNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and DNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: DNA were extracted and qualified at AlmaLab (www.almalab.fi). Soils were extracted following the DNeasy PowerMax Soil Kit protocol (QIAGEN). The exact weight of each soil sample used for extraction was calculated by the mass difference between the 50 mL centrifuge tube (preservation solution preloaded) before and after soil addition. The DNA concentration was quantified using a Qubit 4 Fluorometer together with Qubit DNA IQ Assay Kit (Invitrogen). The DNA quality was verified by 1% agarose gel electrophoresis. DNA extracts were diluted to 1.5 ng uL-1 for amplicon sequencing.

tag: biome

value: Tropical


title: Soil sample 040 from Singapore

status: Public on May 10 2024

type: genomic

country: China

molecule: genomic DNA


title: Soil sample 036 from Singapore


title: DO226_GT20_00446_adipose

type: SRA

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

country: USA

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
Assembly: GRCm38
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.  counts_matrix.csv: raw counts quantified by EMASE and processed by/RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.  vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.  mrna_annots.csv: gene annotation file ENSEMBL version 75.
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

molecule: total RNA

organism: Mus musculus

source_name: adipose

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step.
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: Diversity Outbred mice were sensitized on a high-fat, high-sugar (HFHS) diet

tag: tissue

value: adipose

tag: diet

value: 45 percent  fat


title: Soil sample 034 from Singapore


title: Soil sample 039 from Singapore


title: DO225_GT20_00312_adipose


title: DO228_GT20_00553_adipose


title: Soil sample 035 from Singapore


title: Soil sample 030 from Singapore


title: Soil sample 028 from Singapore


title: Soil sample 024 from Singapore


title: DO227_GT20_00264_adipose


title: DO224_GT20_00631_adipose


title: Soil sample 026 from Singapore


title: Soil sample 032 from Singapore


title: Soil sample 031 from Singapore


title: Soil sample 025 from Singapore


title: Soil sample 027 from Singapore


title: Soil sample 037 from Singapore


title: Soil sample 029 from Singapore


title: DO223_GT20_00465_adipose


title: Soil sample 020 from Singapore


title: Soil sample 019 from Singapore


title: Soil sample 018 from Singapore


title: DO222_GT20_00246_adipose


title: Soil sample 021 from Singapore


title: DO221_GT20_00500_adipose


title: Soil sample 033 from Singapore


title: DO220_GT20_00385_adipose


title: Soil sample 023 from Singapore


title: Soil sample 017 from Singapore


title: Soil sample 022 from Singapore


title: DO219_GT20_00450_adipose


title: Soil sample 016 from Singapore


title: DO215_GT20_00382_adipose


title: DO217_GT20_00357_adipose


title: DO214_GT20_00463_adipose


title: DO218_GT20_00399_adipose


title: Soil sample 015 from Singapore


title: DO213_GT20_00260_adipose


title: Soil sample 014 from Singapore


title: DO212_GT20_00325_adipose


title: Soil sample 012 from Singapore


title: Soil sample 013 from Singapore


title: DO216_GT20_00619_adipose


title: Soil sample 011 from Singapore


title: DO211_GT20_00660_adipose


title: Soil sample 006 from Singapore


title: Soil sample 010 from Singapore


title: Soil sample 007 from Singapore


title: Soil sample 005 from Singapore


title: DO207_GT20_00551_adipose


title: DO208_GT20_00681_adipose


title: DO209_GT20_00476_adipose


title: Soil sample 009 from Singapore


title: DO204_GT20_00386_adipose


title: DO205_GT20_00223_adipose


title: Soil sample 008 from Singapore


title: Soil sample 003 from Singapore


title: DO206_GT20_00641_adipose


title: DO210_GT20_00233_adipose


title: DO203_GT20_00497_adipose


title: DO202_GT20_00245_adipose


title: DO201_GT20_00360_adipose


title: Soil sample 004 from Singapore


title: DO200_GT20_00517_adipose


title: DO199_GT20_00575_adipose


title: DO197_GT20_00268_adipose


title: Soil sample 040 from Lahti, Finland

value: Boreal


title: Soil sample 001 from Singapore


title: Soil sample 002 from Singapore


title: DO196_GT20_00484_adipose


title: Soil sample 036 from Lahti, Finland


title: Soil sample 034 from Lahti, Finland


title: DO195_GT20_00247_adipose


title: DO194_GT20_00652_adipose


title: Soil sample 033 from Lahti, Finland


title: DO193_GT20_00508_adipose


title: DO192_GT20_00486_adipose


title: Soil sample 032 from Lahti, Finland


title: Soil sample 039 from Lahti, Finland


title: Soil sample 035 from Lahti, Finland


title: Soil sample 037 from Lahti, Finland


title: DO190_GT20_00323_adipose


title: DO189_GT20_00432_adipose


title: DO188_GT20_00587_adipose


title: DO187_GT20_00599_adipose


title: DO186_GT20_00516_adipose


title: DO185_GT20_00271_adipose


title: Soil sample 026 from Lahti, Finland


title: Soil sample 025 from Lahti, Finland


title: Soil sample 028 from Lahti, Finland


title: DO183_GT20_00375_adipose


title: Soil sample 029 from Lahti, Finland


title: DO182_GT20_00270_adipose


title: Soil sample 030 from Lahti, Finland


title: Soil sample 024 from Lahti, Finland


title: Soil sample 021 from Lahti, Finland


title: DO181_GT20_00410_adipose


title: Soil sample 027 from Lahti, Finland


title: DO180_GT20_00494_adipose


title: Soil sample 020 from Lahti, Finland


title: DO179_GT20_00578_adipose


title: DO178_GT20_00573_adipose


title: DO184_GT20_00488_adipose


title: Soil sample 022 from Lahti, Finland


title: Soil sample 019 from Lahti, Finland


title: Soil sample 017 from Lahti, Finland


title: Soil sample 018 from Lahti, Finland


title: Soil sample 015 from Lahti, Finland


title: Soil sample 038 from Lahti, Finland


title: Soil sample 023 from Lahti, Finland


title: Soil sample 016 from Lahti, Finland


title: Soil sample 014 from Lahti, Finland


title: DO176_GT20_00532_adipose


title: DO174_GT20_00376_adipose


title: DO175_GT20_00441_adipose


title: DO177_GT20_00287_adipose


title: DO172_GT20_00341_adipose


title: DO171_GT20_00241_adipose


title: Soil sample 013 from Lahti, Finland


title: Soil sample 012 from Lahti, Finland


title: Soil sample 011 from Lahti, Finland


title: DO170_GT20_00498_adipose


title: DO169_GT20_00265_adipose


title: Soil sample 031 from Lahti, Finland


title: DO167_GT20_00574_adipose


title: DO168_GT20_00678_adipose


title: DO165_GT20_00646_adipose


title: DO166_GT20_00512_adipose


title: Soil sample 010 from Lahti, Finland


title: Soil sample 007 from Lahti, Finland


title: Soil sample 009 from Lahti, Finland


title: Soil sample 008 from Lahti, Finland


title: Soil sample 004 from Lahti, Finland


title: Soil sample 006 from Lahti, Finland


title: DO162_GT20_00579_adipose


title: DO161_GT20_00405_adipose


title: Soil sample 002 from Lahti, Finland


title: DO160_GT20_00483_adipose


title: Soil sample 039 from Baltimore, USA

value: Temperate


title: Soil sample 003 from Lahti, Finland


title: Soil sample 001 from Lahti, Finland


title: DO164_GT20_00440_adipose


title: Soil sample 040 from Baltimore, USA


title: DO159_GT20_00461_adipose


title: Soil sample 005 from Lahti, Finland


title: DO158_GT20_00288_adipose


title: Soil sample 038 from Baltimore, USA


title: Soil sample 037 from Baltimore, USA


title: Soil sample 036 from Baltimore, USA


title: DO191_GT20_00697_adipose


title: DO173_GT20_00474_adipose


title: DO157_GT20_00667_adipose


title: DO156_GT20_00414_adipose


title: DO155_GT20_00544_adipose


title: DO153_GT20_00609_adipose


title: Soil sample 033 from Baltimore, USA


title: Soil sample 035 from Baltimore, USA


title: Soil sample 034 from Baltimore, USA


title: Soil sample 031 from Baltimore, USA


title: Soil sample 032 from Baltimore, USA


title: DO152_GT20_00566_adipose


title: DO150_GT20_00286_adipose


title: DO149_GT20_00303_adipose


title: DO163_GT20_00669_adipose


title: DO151_GT20_00694_adipose


title: DO148_GT20_00700_adipose


title: Soil sample 028 from Baltimore, USA


title: Soil sample 030 from Baltimore, USA


title: DO154_GT20_00490_adipose


title: Soil sample 029 from Baltimore, USA


title: DO145_GT20_00273_adipose


title: Soil sample 027 from Baltimore, USA


title: Soil sample 026 from Baltimore, USA


title: DO146_GT20_00231_adipose


title: DO147_GT20_00411_adipose


title: DO144_GT20_00225_adipose


title: DO140_GT20_00226_adipose


title: DO138_GT20_00661_adipose


title: Soil sample 025 from Baltimore, USA


title: DO143_GT20_00695_adipose


title: Soil sample 024 from Baltimore, USA


title: Soil sample 022 from Baltimore, USA


title: Soil sample 023 from Baltimore, USA


title: DO130_GT20_00491_adipose


title: Soil sample 020 from Baltimore, USA


title: Soil sample 021 from Baltimore, USA


title: Soil sample 019 from Baltimore, USA


title: DO141_GT20_00605_adipose


title: Soil sample 014 from Baltimore, USA


title: Soil sample 017 from Baltimore, USA


title: Soil sample 015 from Baltimore, USA


title: Soil sample 016 from Baltimore, USA


title: DO129_GT20_00387_adipose


title: DO137_GT20_00419_adipose


title: Soil sample 009 from Baltimore, USA


title: Soil sample 013 from Baltimore, USA


title: Soil sample 018 from Baltimore, USA


title: DO128_GT20_00662_adipose


title: DO132_GT20_00675_adipose


title: DO131_GT20_00485_adipose


title: DO133_GT20_00568_adipose


title: Soil sample 012 from Baltimore, USA


title: DO122_GT20_00597_adipose


title: DO123_GT20_00443_adipose


title: DO120_GT20_00299_adipose


title: DO126_GT20_00677_adipose


title: DO125_GT20_00439_adipose


title: Soil sample 011 from Baltimore, USA


title: Soil sample 005 from Baltimore, USA


title: Soil sample 010 from Baltimore, USA


title: Soil sample 004 from Baltimore, USA


title: DO116_GT20_00687_adipose


title: DO119_GT20_00359_adipose


title: Soil sample 008 from Baltimore, USA


title: DO124_GT20_00220_adipose


title: DO118_GT20_00515_adipose


title: DO121_GT20_00565_adipose


title: DO115_GT20_00396_adipose


title: Soil sample 007 from Baltimore, USA


title: DO111_GT20_00653_adipose


title: DO108_GT20_00583_adipose


title: Soil sample 006 from Baltimore, USA


title: Soil sample 003 from Baltimore, USA


title: DO114_GT20_00477_adipose


title: Soil sample 001 from Baltimore, USA


title: DO113_GT20_00586_adipose


title: DO109_GT20_00259_adipose


title: DO112_GT20_00680_adipose


title: DO105_GT20_00254_adipose


title: DO107_GT20_00552_adipose


title: Soil sample 002 from Baltimore, USA


title: DO104_GT20_00380_adipose


title: DO097_GT20_00447_adipose


title: DO100_GT20_00320_adipose


title: DO103_GT20_00521_adipose


title: DO101_GT20_00594_adipose


title: DO106_GT20_00331_adipose


title: DO102_GT20_00584_adipose


title: DO096_GT20_00637_adipose


title: DO095_GT20_00613_adipose


title: DO098_GT20_00364_adipose


title: DO094_GT20_00618_adipose


title: DO093_GT20_00529_adipose


title: DO091_GT20_00635_adipose


title: DO092_GT20_00252_adipose


title: DO090_GT20_00275_adipose


title: DO088_GT20_00539_adipose


title: DO087_GT20_00295_adipose


title: DO086_GT20_00545_adipose


title: DO083_GT20_00693_adipose


title: DO082_GT20_00629_adipose


title: DO089_GT20_00470_adipose


title: DO142_GT20_00466_adipose


title: DO099_GT20_00293_adipose


title: DO081_GT20_00230_adipose


title: DO080_GT20_00421_adipose


title: DO079_GT20_00423_adipose


title: DO078_GT20_00294_adipose


title: KFO-primary_chip3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

library_source: transcriptomic single cell

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which were converted to fastq files with bcl2fastq v2.20.0.422
Sequences were demultiplexed using Cogent version 1.0 from TAKARA
Using cutadapt version 2.5, sequences were removed if they had more than 70% N’s, had bases with quality <20 in the 3’ end trimmed,  had N bases trimmed at both ends, were trimmed for various adapters (polyA, polyT, Illumina sequencing regular and reverse complement primers, polyG, SINGV6 and SMART) and were finally discarded if the trimmed reads was shorter than 15 bases
Trimmed sequences were aligned to the genome referencehg38sequenceusing the STAR aligner 2.7.2b using default parameters
Primary, unstranded aligned sequences were counted for all genes using featureCounts version 1.6.4
Gene matrices, metadata and gene info files were generated for all cells in all samples by Cogent version 1.0 from Takara
Assembly: hg38 gene version 107
Supplementary files format and content: GeneMatrix – CSV files with read count per gene for each cell (10 files, one per chip)
Supplementary files format and content: Metadata – CSV files with sample affiliation for each cell and number of reads at different steps of the analysis (10 files, one per chip)
Supplementary files format and content: Gene_info – CSV file with gene information for which reads were counted

organism: Homo sapiens

source_name: primary PDAC

extract_protocol:
Lysis according to iCELL8 single cell system
Nextera based iCELL8 single nuclei
full length cDNA/ iCELL8 Takara

value: primary PDAC


title: DO075_GT20_00469_adipose


title: KFO-primary_chip2


title: KFO-PDX_chip3

source_name: PDAC

value: PDAC


title: DO072_GT20_00227_adipose


title: DO073_GT20_00350_adipose


title: DO074_GT20_00297_adipose


title: KFO-PDX_chip2


title: DO071_GT20_00657_adipose


title: KFO-Organoid_chip4


title: DO070_GT20_00324_adipose


title: KFO-Organoid_chip3


title: DO069_GT20_00634_adipose


title: DO085_GT20_00663_adipose


title: DO084_GT20_00329_adipose


title: DO068_GT20_00665_adipose


title: DO067_GT20_00306_adipose


title: KFO-Organoid_chip1


title: KFO-Organoid_chip2


title: DO066_GT20_00415_adipose


title: DO076_GT20_00344_adipose


title: Day12 mixture, with cMS, rep4

city: Kyoto

first: Koki

last: Yoshimoto

state: Kyoto

department: iCeMS

country: Japan

institute: Kyoto university

data_processing:
Human reference genome (GRCh38.p13.genome.fa)
the number of reads mapped to each gene and transcripts was counted with HISAT2 and featureCounts package with GENCODE (gencode.v36.annotation.gtf)
Supplementary files format and content: tab-delimited text files include readcounts for each Sample

molecule: polyA RNA

source_name: derived from H9 ES cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® and NEBNext Poly(A) mRNA Magnetic Isolation Module were used as library prep kit. Total PCR cycle were 6. For RNA-seq analysis

tag: cell line

value: derived from H9 ES cells

tag: genotype

value: WT

tag: treatment

value: Hepatic and endothelial differentiation

tag: group

value: Day12 mixture, with cMS


title: DO065_GT20_00394_adipose


title: DO063_GT20_00528_adipose


title: Day12 mixture, with cMS, rep2


title: DO064_GT20_00228_adipose


title: Day12 mixture, with cMS, rep1


title: KFO-primary_chip1


title: KFO-PDX_chip1


title: DO061_GT20_00571_adipose


title: DO059_GT20_00340_adipose


title: Day12 mixture, without cMS, rep3

value: Day12 mixture, without cMS


title: DO060_GT20_00258_adipose


title: Day12 mixture, without cMS, rep4


title: Day12 mixture, without cMS, rep1


title: DO057_GT20_00611_adipose


title: Day9 mixture, without cMS, rep5

value: Day9 mixture, without cMS


title: Day12 mixture, without cMS, rep2


title: Day9 mixture, without cMS, rep4


title: Day12 mixture, with cMS, rep5


title: DO056_GT20_00505_adipose


title: Day12 mixture, with cMS, rep3


title: DO054_GT20_00679_adipose


title: Day9 mixture, without cMS, rep2


title: DO055_GT20_00698_adipose


title: Day9 mixture, without cMS, rep3


title: DO052_GT20_00406_adipose


title: DO053_GT20_00699_adipose


title: DO050_GT20_00358_adipose


title: Day12 mixture, without cMS, rep5


title: K562-H3K4me3-G1-rep2_H2VTWBGX9_S8

city: Utrecht

first: Jake

last: Yeung

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K4me3
K562-G1-H3K4me3-100kb.txt.gz

library_source: genomic

data_processing:
fastq files were mapped using BWA-0.7.16a (r1181) to ENSEMBL Build 95
Cells in the top 95% of UMI counts and fraction counts starting with "TA" are kept as "good cells".
Bins were created using 100 kb sliding window with step size of 20 kb.
Genome_build: mm10
Supplementary_files_format_and_content: Genomic bins to cells binned across genomic regions.

extract_protocol:
K562 cells (ATCC CCL-243) were grown in RPMI 1640 Medium, GlutaMAX supplemented with 5%FCS, Pen-Strep and Non-essential amino acids. After harvesting cells were washed 3 times with room temperature PBS before continuing with the scChIC protocol.
Cells were resuspended in 500ul wash buffer (47.5ml H2O RNAse free, 1ml 1M HEPES pH 7.5, 1.5ml 5M NaCl, 3.6ul pure spermidine solution). Aliquot in a 0.5ml protein low-binding tubes (1 per antibody to be used). Following steps are performed on ice.  Cells were pelleted at 600g for 3min and resuspended in 400 ul Wash Buffer 1 (wash buffer with extra 0.05% saponin (Sigma Aldrich), protease inhibitor cocktail (Sigma Aldrich), 4 ul/ml 0.5M EDTA) containing the primary antibody (1:100 dilution for H3K4me1, H3K9me3 and H3K27me3 and 1:200 dilution for H3K4me3, Saponin has to be prepared fresh every time as a 10% solution in PBS). Cells were incubated overnight at 4oC on a roller, before they were washed once with 500 ul Wash Buffer 2 (wash buffer with extra 0.05% saponin, protease inhibitor).  Afterwards cells were resuspended in 500 ul Wash Buffer 2 containing PaMN (3ng/ml) and incubated for 1h at 4C on a roller.  Finally, cells were washed an additional 2 times with 500 ul Wash Buffer 2 before passing it through a 70um cell strainer (Corning, 431751) and sorting them on a JAZZ FACS machine into 384 well plates containing 50nl Wash buffer 3 (Wash buffer containing 0,05% saponin) and 5ul sterile filtered mineral oil (Sigma Aldrich) per well. Small volumes were distributed using a Nanodrop II system (Innovadyme). 50nl of Wash Buffer 3, containing 4uM CaCl2, were added per cell to induce Protein A-MN mediated chromatin digestion that was performed for 30min on ice. Afterwards the reaction was stopped by adding 100nl of a stop solution containing 40mM EGTA (chelates Ca2+ and stops MN), 1.5% NP40 and 10ul 2mg/ml proteinase k (Ambion). Chromatin is subsequently released and PaMN permanently destroyed by proteinase k digestion at 65C for 6h followed by 80C for 20min to heat inactivate proteinase k. Afterwards plates can be stored at -20C until further processing.
DNA fragments are further blunt ended using Klenow large fragment (NEB) and T4 PNK (NEB) in the presence of dNTPs. Afterwards nonintegrated dNTPs are removed using schrimp alkaline phosphatase (NEB) to increase A-tail efficiency. Subsequently blunt fragments are A-Tailed using AmpliTaq™ 360 DNA Polymerase (Thermofisher) in the presence of fresh dATP and T4 PNK (NEB). Next fragments are ligated to T-tail adaptors containing 3 bp UMIs and an 8bp cell barcode (final concentration 9nM from IDT) for 16h at 16C using T4-ligase (NEB). Adaptors were added with a Mosquito HTS (ttp labtech). Ligation products were pooled by centrifugation and cleaned using Ampure XP beads at a bead to sample ratio of 0.8 (Beckman Coulter). The cleaned DNA is then linear amplified by invitro transcription with components of MessageAmp II (Invitrogen) for 16h at 37C. The produced RNA is purified 1-3 times depending on Adaptor dimer contamination using RNA Clean XP beads (Beckman Coulter) at 0.8 beads to sample ratio, followed by RNA fragmentation for 2.5 min at 94C. After another bead cleanup, 20% of the RNA is reverse transcribed with Superscript II (NEB) and PCR amplified to add the Illumina smallRNA barcodes and handles with NEBNext Ultra II Q5 Master Mix. PCR cycles depended on the abundance of the histone modification assayed and the number of RNA cleanup cycles after IVT needed (8-10 for H3K9me3 and H3K27me3 10-12 for H3K4me1 and 12-15 for H3K4me3).

tag: antibody


title: Day9 mixture, without cMS, rep1


title: DO058_GT20_00442_adipose


title: K562-H3K4me3-G1-rep3_AH3T55BGX9_S2


title: DO051_GT20_00274_adipose


title: DO048_GT20_00626_adipose


title: K562-H3K9me3-G1-rep1_H2VTWBGX9_S3

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K9me3
K562-G1-H3K9me3-100kb.txt.gz


title: K562-H3K27me3-G1-rep3_AH3T55BGX9_S4

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K27me3
K562-G1-H3K27me3-100kb.txt.gz


title: DO046_GT20_00257_adipose


title: DO049_GT20_00354_adipose


title: DO047_GT20_00409_adipose


title: K562-H3K4me1-G1-rep3_AH2GNLBGX9_S3

description:
genomicDNA_cut_from_MNase-ProteinA_with_staining_of_H3K4me1
K562-G1-H3K4me1-100kb.txt.gz


title: DO062_GT20_00585_adipose


title: DO044_GT20_00418_adipose


title: DO043_GT20_00655_adipose


title: K562-H3K4me3-G1-rep1_H2VTWBGX9_S2


title: DO042_GT20_00347_adipose


title: K562-H3K27me3-G1-rep1_H2VTWBGX9_S4


title: DO041_GT20_00547_adipose


title: K562-H3K9me3-G1-rep3_AH3T55BGX9_S3


title: DO040_GT20_00397_adipose


title: DO039_GT20_00543_adipose


title: K562-H3K4me1-G1-rep1_H2VTWBGX9_S1


title: DO038_GT20_00533_adipose


title: K562-H3K4me1-G1-rep2_H2VTWBGX9_S6


title: K562-H3K4me1-G1-rep3_AH3T55BGX9_S1


title: DO037_GT20_00630_adipose


title: K562-H3K4me3-G1-rep3_AH2GNLBGX9_S4


title: K562-H3K27me3-G1-rep2_H2VTWBGX9_S5


title: DO034_GT20_00369_adipose


title: H3K27ac_E2Rln_replicate2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bed” files for later Metagene and read-density analyses by using the BEDTools software package  (Quinlan et al, 2010).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: mouse myometrium

growth_protocol: Samples were collected for each of the four treatment time points (vehicle, E2, Rln, and E2+Rln) from ovariectomized mice treated for 1 hour.

extract_protocol:
Pools of frozen myometrial tissue (5 myometrium per pool; 60 to 80 mg of tissue) were powdered using a metal pulverizer.  The powdered myometrial pool was immediately resuspended in 1% formaldehyde in phosphate-buffered saline (PBS) with a volume of 10 mL per pool, then incubated on a rotating platform at room temperature for 10 min.  Crosslinking was quenched by adding 5 mL per pool of 2.5 M glycine, with a subsequent 5 min incubation at room temperature.  The crosslinked tissue was collected by centrifugation at 1000 x g for 3 min at room temperature.  The supernatant was decanted, and the tissue was resuspended in 4°C PBS with added protease inhibitor cocktail (Roche Molecular Biochemicals) at 10 mL per pool, with incubation on ice for 2 min.  The samples were centrifuged at 1000 x g for 3 min at 4°C.  The PBS wash was repeated, and the tissue was resuspended in 2.5 mL per pool of homogenization buffer (50 mM Tris-HCl pH 7.5, 1% Nonidet P-40, 0.25% deoxycholic acid, 1 mM EDTA) supplemented with proteinase inhibitor cocktail. The crosslinked tissue was homogenized using a cooled blade homogenizer (Power Gen25).  The pellet was collected by centrifugation at 1000 x g for 5 min at 4°C.  The supernatant was decanted and the pellet was resuspended in 1 mL per pool of Farnham Buffer (5 mM PIPES, pH 8.0, 85 mM KCl, 0.5% Nonidet P-40, 1 mM DTT, 0.1 mM PMSF) supplemented with proteinase inhibitor cocktail by mixing five times with a pipettor and then incubated on ice for 10 min.  The chromatin was pelleted by centrifugation for 1000 x g for 10 min at 4°C and resuspended in SDS Lysis Buffer (50 mM Tris-HCl pH 7.9, 10 mM EDTA, 1% SDS, 1 mM DTT) supplemented with proteinase inhibitor cocktail and histone deacetylases inhibitors (10 mM sodium butyrate, 5 mM nicotinamide).  Resuspended chromatin was incubated on ice for 10 min, split into 300 mL aliquots, and sonicated on ice using a Bioruptor UCD-200 (Diagenode) on the high setting for 9 cycles, 30 sec on and 30 sec off with 1 min rest, 4 times, to obtain genomic DNA fragments of approximately 200 to 400 bp, as determined by gel electrophoresis.  Sonicated chromatin was centrifuged at maximum speed in a microcentrifuge for 1 min at 4°C to remove insoluble debris, and the soluble chromatin supernatant was flash frozen in liquid N2 and stored at -80°C until use. Chromatin was diluted 1:9 with Dilution Buffer (20 mM Tris-HCl pH 7.9, 300 mM NaCl, 2 mM EDTA, 0.5% Triton X-100, 1 mM DTT, 0.2 mM PMSF) supplemented with proteinase inhibitor cocktail and histone deacetylases inhibitors.  The diluted chromatin was pre-cleared with 20 mL/mL protein A-agarose beads (ThermoFisher Scientific; 50% slurry in 10 mM Tris-HCl pH 8.1; 1 mM EDTA) on a nutator for 1 hour at 4°C.  The pre-cleared chromatin was centrifuged in a microcentrifuge at 1000 x g for 3 min at 4°C.  The pre-cleared supernatant was divided into input (2.5%) and a 1 mL aliquot for immunoprecipitation.  Immunoprecipitation was performed overnight at 4°C using the polyclonal antibodies for ERa, H3K27ac, or H3K4me1.  For a control, rabbit IgG (BioRad; PRABP01) was added at 1:200. Immune complexes were collected by the addition of 80 mL of protein A-agarose beads (Cell Signaling Technology; 9863) with an additional 2 hours incubation at 4°C with mixing.  The samples were centrifuged in a microcentrifuge at 500 x g at 4°C for 1 min to collect the resin.  The resin was washed four times for 10 min each in Low Salt Wash Buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100), four times for 10 min each  in High Salt Wash Buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100], one time with LiCl Wash Buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% Nonidet P-40, 1% sodium deoxycholate), and one time in TE.  All buffers were supplemented with proteinase inhibitor cocktail and histone deacetylases inhibitors.  The cross-linked chromatin was then eluted twice using Elution Buffer (1% SDS and 100 mM sodium bicarbonate) at room temperature for 15 min.  The eluted chromatin was heated at 65°C overnight in Elution Buffer supplemented with 100 mM NaCl to reverse the formaldehyde crosslinking.  RNase was added to 3 mg/mL final concentration was added and incubated at 37°C for 30 min, followed by inactivation with Tris-HCl pH 7.9, 5 mM EDTA, 50 mg/mL proteinase K at 55°C for 2 hours.  The immunoprecipitated DNA fragments were purified by phenol:chloroform extraction, followed by ethanol precipitation.  The purified ChIPed DNA was processed to prepare ChIP-seq libraries.
ChIP-seq libraries were generated from two biological replicates for each condition as described previously (Franco et al., 2015; Luo et al., 2014).  Immunoprecipitated (ChIPed) DNA was purified further by polyethylene glycol (PEG)-mediated precipitation (Lis and Schleif, 1975) using PEG Precipitation Solution (20% in 20 mM Tris-HCl pH 7.9, 4 mM EDTA, 2.5 M NaCl).  After purification, 5 ng (for ERa) and 10 ng (for H3K27ac and H3K4me1) of ChIPed DNA for each treatment condition was used to generate libraries for sequencing, as previously described with some minor modifications (Luo et al., 2014).  Briefly, the ChIPed DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E.coli DNA polymerase.  The A-modified DNA was ligated with Illumina sequencing adapters using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250 ± 25 bp) was size-selected using a bead-based method with magnetic beads (AmPure XP beads, Beckman Coulter) isolate DNA fragment sizes of interest.  The size-selected DNA was amplified by PCR (9 to 11 cycles as determined empirically) and purified using AmPure XP beads.  The final libraries were run on agarose gel, and extracted using QIAquick gel extraction kit (Qiagen).  The final libraries were subjected to QC (size, purity, adapter contamination).  The quality of libraries was assessed using a High Sensitivity D1000 screen tape on a 2200 TapeStation (Agilent) and quantified using a Qubit dsDNA HS assay kit (ThermoFisher Scientific).  The libraries with unique adapter barcodes were multiplexed and sequenced on an Illumina HiSeq 2500 (single-end, 75 base reads) to a depth of ~40 M reads per condition.

value: mouse myometrium

value: H3K27ac ChIP enriched genomic DNA from mouse myometrium treated with E2 and Rln


title: K562-H3K9me3-G1-rep3_AH2GNLBGX9_S5


title: H3K27ac_E2Rln_replicate1


title: K562-H3K27me3-G1-rep3_AH2GNLBGX9_S5


title: DO036_GT20_00612_adipose


title: DO035_GT20_00684_adipose


title: DO032_GT20_00538_adipose


title: DO031_GT20_00417_adipose


title: DO033_GT20_00256_adipose


title: H3K27ac_Rln_replicate1

value: H3K27ac ChIP enriched genomic DNA from mouse myometrium treated with Rln


title: H3K27ac_E2_replicate2

value: H3K27ac ChIP enriched genomic DNA from mouse myometrium treated with E2


title: H3K27ac_E2_replicate1


title: DO028_GT20_00638_adipose


title: H3K27ac_Veh_replicate2

value: H3K27ac ChIP enriched genomic DNA from mouse myometrium treated with saline


title: DO030_GT20_00238_adipose

value: adipose


title: DO026_GT20_00407_adipose

value: 45 percent  fat


title: H3K4me1_E2Rln_replicate2

value: H3K4me1 ChIP enriched genomic DNA from mouse myometrium treated with E2 and Rln


title: H3K27ac_Veh_replicate1


title: DO025_GT20_00592_adipose


title: DO024_GT20_00649_adipose


title: H3K4me1_Rln_replicate2

value: H3K4me1 ChIP enriched genomic DNA from mouse myometrium treated with Rln


title: DO027_GT20_00670_adipose


title: K562-H3K9me3-G1-rep2_H2VTWBGX9_S9


title: H3K27ac_Rln_replicate2


title: DO023_GT20_00504_adipose


title: H3K4me1_Rln_replicate1


title: DO022_GT20_00475_adipose


title: H3K4me1_E2_replicate1

value: H3K4me1 ChIP enriched genomic DNA from mouse myometrium treated with E2


title: DO021_GT20_00377_adipose


title: H3K4me1_E2_replicate2


title: H3K4me1_Veh_replicate2

value: H3K4me1 ChIP enriched genomic DNA from mouse myometrium treated with saline


title: ER_E2Rln_replicate1

value: ER ChIP enriched genomic DNA from mouse myometrium treated with E2 and Rln


title: H3K4me1_Veh_replicate1


title: Spinal cord, 3d_SCI, 215s_E16

city: Solna

first: Christian

last: Göritz

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institutet

data_processing:
see Smart-Seq3 protocol  (Hagemann-Jensen et al. 2020).
Assembly: mm10
Supplementary files format and content: NN_Glast_B_d0d3d5_count_matrix.csv
Supplementary files format and content: NN_sampleinfo_scs.csv

source_name: Spinal cord

extract_protocol:
Preparation of single-cell cell suspensions and myelin removal was  performed using adult brain dissociation kit (130-107-677, Miltenyi), followed by Smart-seq 3 library preparation protocol. In summary, uninjured, and 3 days and 5 days after spinal cord crush GLAST-CreERT2;R26R-tdTomato;Pdgfrb-eGFP animals were euthanized by intraperitoneal injection of sodium pentobarbital and transcardially perfused with cold Hank's Balanced Salt Solution without calcium or magnesium (HBSS) (Invitrogen). The spinal cord was carefully dissected out of the vertebrae and the crush injury segment was separated from the uninjured spinal cord tissue and treated separately hereafter. After removal of the outer meningeal layers, the tissue was mechanically dissociated with a razor blade on a glass Petri dish and immediately transferred to cold HBSS. This step was followed by enzymatic digestion. Following dissociation cell pellets were resuspended in cold MACS buffer and magnetic myelin removal beads (Miltenyi Biotech, 130-096-433) and incubated for 15 min at 4°C. The cells were washed and run over MACS MS columns (Miltenyi Biotech, 130-042-201) on a magnetic stand according to the manufacturer’s instructions. The cells in the flow through were collected, spun down, resuspended in FACS buffer (2% FBS in PBS) and kept on ice until further processing. The single-cell suspensions generated from GLAST-CreERT2;R26R-tdTomato;Pdgfrb-eGFP animals were subjected to fluorescence activated cell sorting (FACS). Based on reporter gene expression, tdTomato+EGFP+ and tdTomato-EGFP+ cells were collected into 384 plates with Smart-seq 3 lysis buffer mix, followed by a brief centrifugation (1 min, 1500 rpm) and stored at -80 °C until further processing. Cell sorting was performed on a FACSAria III Cell Sorter (BD Biosciences). Singlet discrimination was performed using plots for forward scatter (FSC-A versus FSC-H) and side scatter (SSC-W versus SSC-H), and dead cells were excluded by SYTOX Blue Dead Cell Stain (ThermoFisher Scientific, S34857).
Single cells were processed to cDNA libraries according to the Smart-Seq3 protocol  (Hagemann-Jensen et al. 2020).

value: Spinal cord

tag: cell type

value: Perivascular cells

tag: Sex

value: female

tag: sorted population

value: EGFP+; tdTomato-


title: Spinal cord, 3d_SCI, 215s_E19


title: Spinal cord, 3d_SCI, 215s_E24


title: Spinal cord, 3d_SCI, 215s_E23


title: ER_Rln_replicate2

value: ER ChIP enriched genomic DNA from mouse myometrium treated with Rln


title: Spinal cord, 3d_SCI, 215s_E17


title: ER_Rln_replicate1

value: mouse myometrium


title: ER_E2Rln_replicate2


title: H3K4me1_E2Rln_replicate1


title: Spinal cord, 3d_SCI, 215s_E15


title: Spinal cord, 3d_SCI, 215s_E14


title: ER_Veh_replicate2

value: ER ChIP enriched genomic DNA from mouse myometrium treated with saline


title: ER_E2_replicate1

value: ER ChIP enriched genomic DNA from mouse myometrium treated with E2


title: Spinal cord, 3d_SCI, 215s_E12


title: ER_E2_replicate2


title: Spinal cord, 3d_SCI, 215s_E11


title: Spinal cord, 3d_SCI, 215s_E10


title: Input_E2Rln_replicate2

value: genomic DNA from mouse myometrium treated with E2 Rln


title: ER_Veh_replicate1


title: Spinal cord, 3d_SCI, 215s_E08


title: Spinal cord, 3d_SCI, 215s_E18


title: Spinal cord, 3d_SCI, 215s_E07


title: Input_Rln_replicate2

value: genomic DNA from mouse myometrium treated with Rln


title: Spinal cord, 3d_SCI, 215s_E05


title: Spinal cord, 3d_SCI, 215s_E04


title: Input_Rln_replicate1


title: Input_E2_replicate1

value: genomic DNA from mouse myometrium treated with E2


title: Spinal cord, 3d_SCI, 215s_E03


title: Spinal cord, 3d_SCI, 215s_D21


title: Spinal cord, 3d_SCI, 215s_D22


title: Spinal cord, 3d_SCI, 215s_D23


title: Input_Veh_replicate2

value: genomic DNA from mouse myometrium


title: Input_Veh_replicate1


title: Spinal cord, 3d_SCI, 215s_E02


title: Spinal cord, 3d_SCI, 215s_E01


title: Spinal cord, Injury, P6981_1832

data_processing:
Clustering was done by 'cBot' and samples were sequenced on Illumina HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. Mus musculus, GRCm38 was used as reference genome.   We used a single-cell RNA sequencing snakemake workflow (“lts_workflows_sm_scrnaseq”) for alignment, quantification and quality control using resources as follows: The reads were aligned to the mouse (mm10) genome using STAR 2.5.3a (Dobin et al., 2013) and transcripts quantified in terms of Reads Per Kilobase of transcript per Million mapped reads (RPKM) using rpkmforgenes v1.0.1  (Ramsköld et al., 2009) and RSEM to estimate gene and isoform expression levels v1.2.28  (Li and Dewey, 2011). RSeQC V2.6.4  (Wang et al., 2012) Multiqc v0.9.1 were used for quality control. To filter out low quality libraries the following filtering criteria for quality control were applied: star_Uniquely mapped: < mean - 2 sd, gene_detection : > mean - 2 sd & < mean + 2 sd, count_gene : < mean - 2 sd, gene_correlation_max : < mean - 2 sd. Cells that failed for 2 of the criteria were filtered out (25 cells, 2.89% of 864, the total number of cells).
Assembly: mm10
Supplementary files format and content: rpkmforgenes_counts.tab
Supplementary files format and content: 170706_sampleinfo_scs.csv

extract_protocol:
Preparation of single-cell cell suspension and myelin removal was adapted from previously published protocols (Lovatt et al., 2007; Orre et al., 2014). In summary, the procedure was: 5 days after spinal cord crush injury, animals were euthanized by intraperitoneal injection of sodium pentobarbital (200mg/Kg, 100ul i.p., APL) and transcardially perfused with cold Hank's Balanced Salt Solution without calcium or magnesium (HBSS) (Invitrogen). The vertebral column was immediately removed to cold HBSS, the spinal cord was carefully dissected out of the vertebrae and the crush injury segment was separated from the uninjured spinal cord and treated separately hereafter. After removal of the outer meningeal layers, the tissue was dissociated mechanically with a razor blade on a glass petri dish and immediately transferred to cold HBSS. Followed by enzymatic digestion with papain at a final concentration of 8 U/mL with 80 Kunitz units/mL DNase I (Sigma-Aldrich, D4263) in Ca2+/Mg2+-free piperazine-N,N′-bis(2-ethanesulfonic acid) (PIPES)/cysteine -based buffer, pH 7.4, for 40min at 37°C, 350rpm on a ThermoMixer® (Eppendorf). The tissue was carefully triturated and incubated for additional 5min. The cell suspension was passed through a 70μmCell Strainer (Corning), washed with Minimum Essential Media (MEM) with 1% bovine serum albumin (BSA) and spun down at 200g for 5min at 4°C. The cells were resuspended in MEM and centrifuged over a 90% Percoll gradient (GE Healthcare, 17-0891-01) at 250g for 15min at 4°C. Cells in the lipid layer and below were diluted 5 times in MEM with 1% BSA and spun in a 15mL tube at 250g for 10min at 4°C. All supernatant including the lipid layer were carefully removed and the pellet resuspended in cold MACS Buffer and magnetic Myelin removal beads (Miltenyi biotech, 130-096-433) and incubated for 15min at 4°C. The cells were washed and run over MACS MS columns (Miltenyi biotech, 130-042-201) on a magnetic stand according to the manufacturer’s instructions. The flow through cells were collected, spun down and resuspended in FACS buffer. The single cell suspensions derived from normal spinal cord and injury segments were subject to FACS (fluorescence activated cell sorting) into GLAST-CreER-tomato+/Pdgfrb-eGFP+ double positive and Pdgfrb-eGFP+ single cells, into 96-well plates with Cell lysis buffer (Clonetech, 635013) and frozen to -80°C. Cell sorting was performed on a FACSAria III Cell Sorter system (BD Biosciences). Singlet discrimination was performed using plots for forward scatter (FSC-A versus FSC-H) and side scatter (SSC-W versus SSC-H), dead cells were excluded by SYTOX Blue Dead Cell Stain (ThermoFisher Scientific, S34857).
Single cells were processed to cDNA libraries according to the Smart-Seq2 protocol  (Picelli et al. 2014). Tn5 tagmentation was performed using the Nextera XT DNA library Preparation Kit (Illumina, FC-131-1002) using dual indexes (i7 and i5).

value: male

value: EGFP+; tdTomato+


title: Spinal cord, Injury, P6981_1831


title: Spinal cord, Injury, P6981_1829


title: Spinal cord, 3d_SCI, 215s_D18


title: Spinal cord, Injury, P6981_1830


title: Spinal cord, Injury, P6981_1828


title: Spinal cord, 3d_SCI, 215s_D14


title: Spinal cord, 3d_SCI, 215s_D20


title: Spinal cord, Injury, P6981_1826


title: Input_E2Rln_replicate1


title: Spinal cord, Injury, P6981_1824


title: Input_E2_replicate2


title: Spinal cord, 3d_SCI, 215s_D13


title: Spinal cord, Injury, P6981_1827


title: Spinal cord, Injury, P6981_1823


title: Spinal cord, Injury, P6981_1822


title: Spinal cord, Injury, P6981_1825


title: Spinal cord, 3d_SCI, 215s_D10


title: Spinal cord, 3d_SCI, 215s_D09


title: Spinal cord, 3d_SCI, 215s_D08


title: Spinal cord, Injury, P6981_1821


title: Spinal cord, 3d_SCI, 215s_D07


title: Spinal cord, 3d_SCI, 215s_D05


title: Spinal cord, 3d_SCI, 215s_D02


title: Spinal cord, Injury, P6981_1820


title: Spinal cord, Injury, P6981_1819


title: Spinal cord, 3d_SCI, 215s_D01


title: Spinal cord, Injury, P6981_1817


title: Spinal cord, 3d_SCI, 215s_D15


title: Spinal cord, 3d_SCI, 215s_C21


title: Spinal cord, 3d_SCI, 215s_C24


title: Spinal cord, Injury, P6981_1816


title: Spinal cord, 3d_SCI, 215s_C20


title: Spinal cord, Injury, P6981_1815


title: Spinal cord, Injury, P6981_1818


title: Spinal cord, Injury, P6981_1814


title: Spinal cord, Injury, P6981_1813


title: Spinal cord, 3d_SCI, 215s_C16


title: Spinal cord, 3d_SCI, 215s_C18


title: Spinal cord, 3d_SCI, 215s_C15


title: Spinal cord, Injury, P6981_1811


title: Spinal cord, Injury, P6981_1812


title: Spinal cord, 3d_SCI, 215s_C14


title: Spinal cord, Injury, P6981_1810


title: Spinal cord, 3d_SCI, 215s_C12


title: Spinal cord, Injury, P6981_1809


title: Spinal cord, 3d_SCI, 215s_C06


title: Spinal cord, Injury, P6981_1808


title: Spinal cord, 3d_SCI, 215s_C05


title: Spinal cord, 3d_SCI, 215s_C10


title: Spinal cord, Injury, P6981_1807


title: Spinal cord, Injury, P6981_1806


title: Spinal cord, Injury, P6981_1805


title: Spinal cord, 3d_SCI, 215s_C04


title: Spinal cord, Injury, P6981_1804


title: Spinal cord, 3d_SCI, 215s_C03


title: Spinal cord, 3d_SCI, 215s_C02


title: Spinal cord, 3d_SCI, 215s_B23


title: Spinal cord, 3d_SCI, 215s_B22


title: Spinal cord, Injury, P6981_1802


title: Spinal cord, 3d_SCI, 215s_B21


title: Spinal cord, Injury, P6981_1801


title: Spinal cord, Injury, P6981_1803


title: Spinal cord, Injury, P6981_1799


title: Spinal cord, 3d_SCI, 215s_B19


title: Spinal cord, 3d_SCI, 215s_B18


title: Spinal cord, Injury, P6981_1800


title: Spinal cord, 3d_SCI, 215s_B20


title: Spinal cord, Injury, P6981_1798


title: Spinal cord, Injury, P6981_1797


title: Spinal cord, 3d_SCI, 215s_B17


title: Spinal cord, Injury, P6981_1796


title: Spinal cord, 3d_SCI, 215s_B15


title: Spinal cord, Injury, P6981_1794


title: Spinal cord, 3d_SCI, 215s_B14


title: Spinal cord, 3d_SCI, 215s_B13


title: Spinal cord, Injury, P6981_1793


title: Spinal cord, Injury, P6981_1792


title: Spinal cord, Injury, P6981_1791


title: Spinal cord, 3d_SCI, 215s_B12


title: Spinal cord, 3d_SCI, 215s_B24


title: Spinal cord, 3d_SCI, 215s_B11


title: Spinal cord, Injury, P6981_1789


title: Spinal cord, 3d_SCI, 215s_B10


title: Spinal cord, Injury, P6981_1790


title: Spinal cord, 3d_SCI, 215s_B09


title: Spinal cord, Injury, P6981_1787


title: Spinal cord, 3d_SCI, 215s_B08


title: Spinal cord, Injury, P6981_1786


title: Spinal cord, Injury, P6981_1784


title: Spinal cord, 3d_SCI, 215s_B01


title: Spinal cord, 3d_SCI, 215s_B06


title: Spinal cord, 3d_SCI, 215s_B16


title: Spinal cord, 3d_SCI, 215s_A24


title: Spinal cord, Injury, P6981_1783


title: Spinal cord, 3d_SCI, 215s_A23


title: Spinal cord, Injury, P6981_1795


title: Spinal cord, Injury, P6981_1782


title: Spinal cord, 3d_SCI, 215s_A20


title: Spinal cord, Injury, P6981_1781


title: Spinal cord, 3d_SCI, 215s_A18


title: Spinal cord, Injury, P6981_1779


title: Spinal cord, 3d_SCI, 215s_A14


title: Spinal cord, 3d_SCI, 215s_A16


title: Spinal cord, Injury, P6981_1780


title: Spinal cord, Injury, P6981_1778


title: Spinal cord, 3d_SCI, 215s_A15


title: Spinal cord, Injury, P6981_1777


title: Spinal cord, 3d_SCI, 215s_B07


title: Spinal cord, 3d_SCI, 215s_A12


title: Spinal cord, Injury, P6981_1775


title: Spinal cord, 3d_SCI, 215s_A13


title: Spinal cord, Injury, P6981_1776


title: Spinal cord, 3d_SCI, 215s_A10


title: Spinal cord, Injury, P6981_1774


title: Spinal cord, Injury, P6981_1773


title: Spinal cord, Injury, P6981_1788


title: Spinal cord, Injury, P6981_1785


title: Spinal cord, 3d_SCI, 215s_A06


title: Spinal cord, Injury, P6981_1772


title: Spinal cord, Injury, P6981_1771


title: Spinal cord, Injury, P6981_1770


title: Spinal cord, 3d_SCI, 215s_A11


title: Spinal cord, 3d_SCI, 215s_A03


title: Spinal cord, Uninjured, 213s_P20

value: Uninjured


title: Spinal cord, Injury, P6981_1769


title: Spinal cord, Injury, P6981_1767


title: Spinal cord, Injury, P6981_1768


title: Spinal cord, Injury, P6981_1766


title: Spinal cord, Uninjured, 213s_P11


title: Spinal cord, Injury, P6981_1765


title: Spinal cord, Uninjured, 213s_P09


title: Spinal cord, Uninjured, 213s_P18


title: Spinal cord, Injury, P6981_1764


title: Spinal cord, Uninjured, 213s_P15


title: Spinal cord, Uninjured, 213s_P17


title: Spinal cord, Uninjured, 213s_P07


title: Spinal cord, Injury, P6981_1761


title: Spinal cord, Uninjured, 213s_P06


title: Spinal cord, Injury, P6981_1763


title: Spinal cord, Uninjured, 213s_P05


title: Spinal cord, Injury, P6981_1759


title: Spinal cord, Injury, P6981_1760


title: Spinal cord, Uninjured, 213s_P08


title: Spinal cord, 3d_SCI, 215s_A09


title: Spinal cord, Injury, P6981_1762


title: Spinal cord, Uninjured, 213s_P03


title: Spinal cord, Uninjured, 213s_P04


title: Spinal cord, Injury, P6981_1756


title: Spinal cord, Injury, P6981_1757


title: Spinal cord, Injury, P6981_1758


title: Spinal cord, Uninjured, 213s_P01


title: Spinal cord, Uninjured, 213s_O20


title: Spinal cord, Injury, P6981_1754


title: Spinal cord, Uninjured, 213s_O17


title: Spinal cord, Uninjured, 213s_O15


title: Spinal cord, Uninjured, 213s_P13


title: Spinal cord, Injury, P6981_1753


title: Spinal cord, Injury, P6981_1752


title: Spinal cord, Injury, P6981_1751


title: Spinal cord, Injury, P6981_1750


title: Spinal cord, Uninjured, 213s_O13


title: Spinal cord, Uninjured, 213s_O10


title: Spinal cord, Injury, P6981_1748


title: Spinal cord, Injury, P6981_1749


title: Spinal cord, Uninjured, 213s_O02


title: Spinal cord, Uninjured, 213s_O06


title: Spinal cord, Injury, P6981_1746


title: Spinal cord, Uninjured, 213s_N22


title: Spinal cord, Uninjured, 213s_N16


title: Spinal cord, Injury, P6981_1745


title: Spinal cord, Injury, P6981_1747


title: Spinal cord, Uninjured, 213s_N19


title: Spinal cord, Injury, P6981_1743


title: Spinal cord, Injury, P6981_1755


title: Spinal cord, Injury, P6981_1744


title: Spinal cord, Uninjured, 213s_N14


title: Spinal cord, Injury, P6981_1739


title: Spinal cord, Injury, P6981_1742


title: Spinal cord, Injury, P6981_1740


title: Spinal cord, Uninjured, 213s_N10


title: Spinal cord, Uninjured, 213s_N12


title: Spinal cord, Uninjured, 213s_N09


title: Spinal cord, Uninjured, 213s_O11


title: Spinal cord, Uninjured, 213s_N13


title: Spinal cord, Uninjured, 213s_N05


title: Spinal cord, Injury, P6981_1738


title: Spinal cord, Uninjured, 213s_N08


title: Spinal cord, Uninjured, 213s_N04


title: Spinal cord, Injury, P6981_1737


title: Spinal cord, Injury, P6981_1736


title: Spinal cord, Uninjured, 213s_N02


title: Spinal cord, Uninjured, 213s_N01


title: Spinal cord, Injury, P6981_1741


title: Spinal cord, Injury, P6981_1733


title: Spinal cord, Uninjured, 213s_M16


title: Spinal cord, Uninjured, 213s_M19


title: Spinal cord, Injury, P6981_1731


title: Spinal cord, Uninjured, 213s_M12


title: Spinal cord, Injury, P6981_1732


title: Spinal cord, Uninjured, 213s_M11


title: Spinal cord, Injury, P6981_1730


title: Spinal cord, Uninjured, 213s_M10


title: Spinal cord, Injury, P6981_1729


title: Spinal cord, Injury, P6981_1725


title: Spinal cord, Uninjured, 213s_M08


title: Spinal cord, Injury, P6981_1727


title: Spinal cord, Injury, P6981_1726


title: Spinal cord, Injury, P6981_1724


title: Spinal cord, Injury, P6981_1735


title: Spinal cord, Injury, P6981_1723


title: Spinal cord, Injury, P6981_1722


title: Spinal cord, Uninjured, 213s_M03


title: Spinal cord, Injury, P6981_1734


title: Spinal cord, Uninjured, 213s_M04


title: Spinal cord, Injury, P6981_1728


title: Spinal cord, Uninjured, 213s_M21


title: Spinal cord, Uninjured, 213s_M14


title: Spinal cord, Uninjured, 213s_L23


title: Spinal cord, Injury, P6981_1721


title: Spinal cord, Uninjured, 213s_L22


title: Spinal cord, Injury, P6981_1719


title: Spinal cord, Injury, P6981_1720


title: Spinal cord, Uninjured, 213s_L18


title: Spinal cord, Injury, P6981_1718


title: Spinal cord, Uninjured, 213s_M09


title: Spinal cord, Uninjured, 213s_L14


title: Spinal cord, Injury, P6981_1717


title: Spinal cord, Uninjured, 213s_L16


title: Spinal cord, Uninjured, 213s_L12


title: Spinal cord, Uninjured, 213s_M07


title: Spinal cord, Injury, P6981_1716


title: Spinal cord, Uninjured, 213s_M01


title: Spinal cord, Injury, P6981_1715


title: Spinal cord, Uninjured, 213s_L10


title: Spinal cord, Injury, P6981_1712


title: Spinal cord, Uninjured, 213s_L07


title: Spinal cord, Uninjured, 213s_L05


title: Spinal cord, Uninjured, 213s_L08


title: Spinal cord, Uninjured, 213s_L11


title: Spinal cord, Injury, P6981_1714


title: Spinal cord, Injury, P6981_1710


title: Spinal cord, Uninjured, 213s_L21


title: Spinal cord, Uninjured, 213s_O14


title: Spinal cord, Injury, P6981_1709


title: Spinal cord, Injury, P6981_1707


title: Spinal cord, Uninjured, 213s_L04


title: Spinal cord, Uninjured, 213s_L03


title: Spinal cord, Injury, P6981_1708


title: Spinal cord, Injury, P6981_1706


title: Spinal cord, Uninjured, 213s_L01


title: Spinal cord, Injury, P6981_1702


title: Spinal cord, Uninjured, 213s_K20


title: Spinal cord, Injury, P6981_1704


title: Spinal cord, Injury, P6981_1713


title: Spinal cord, Uninjured, 213s_K24


title: Spinal cord, Uninjured, 213s_K18


title: Spinal cord, Injury, P6981_1705


title: Spinal cord, Uninjured, 213s_K22


title: Spinal cord, Injury, P6981_1703


title: Spinal cord, Injury, P6981_1701


title: Spinal cord, Injury, P6981_1711


title: Spinal cord, Injury, P6981_1699


title: Spinal cord, Injury, P6981_1700


title: Spinal cord, Uninjured, 213s_K16


title: Spinal cord, Uninjured, 213s_K17


title: Spinal cord, Uninjured, 213s_K14


title: Spinal cord, Injury, P6981_1697


title: Spinal cord, Injury, P6981_1696


title: Spinal cord, Uninjured, 213s_L02


title: Spinal cord, Uninjured, 213s_K12


title: Spinal cord, Injury, P6981_1694


title: Spinal cord, Uninjured, 213s_K11


title: Spinal cord, Injury, P6981_1695


title: Spinal cord, Uninjured, 213s_K09


title: Spinal cord, Injury, P6981_1693


title: Spinal cord, Uninjured, 213s_K05


title: Spinal cord, Uninjured, 213s_K04


title: Spinal cord, Injury, P6981_1692


title: Spinal cord, Injury, P6981_1691


title: Spinal cord, Uninjured, 213s_K03


title: Spinal cord, Injury, P6981_1690


title: Spinal cord, Uninjured, 213s_K01


title: Spinal cord, Injury, P6981_1689


title: Spinal cord, Uninjured, 213s_J23


title: Spinal cord, Uninjured, 213s_K15


title: Spinal cord, Injury, P6981_1688


title: Spinal cord, Uninjured, 213s_J22


title: Spinal cord, Injury, P6981_1687


title: Spinal cord, Uninjured, 213s_J15


title: Spinal cord, Uninjured, 213s_K13


title: Spinal cord, Injury, P6981_1686


title: Spinal cord, Injury, P6981_1685


title: Spinal cord, Uninjured, 213s_J17


title: Spinal cord, Uninjured, 213s_J20


title: Spinal cord, Injury, P6981_1683


title: Spinal cord, Uninjured, 213s_J13


title: Spinal cord, Uninjured, 213s_J11


title: Spinal cord, Injury, P6981_1684


title: Spinal cord, Injury, P6981_1682


title: Spinal cord, Uninjured, 213s_J09


title: Spinal cord, Injury, P6981_1680


title: Spinal cord, Injury, P6981_1681


title: Spinal cord, Injury, P6981_1679


title: Spinal cord, Uninjured, 213s_J07


title: Spinal cord, Uninjured, 213s_J05


title: Spinal cord, Injury, P6981_1678


title: Spinal cord, Uninjured, 213s_J01


title: Spinal cord, Injury, P6981_1677


title: Spinal cord, Uninjured, 213s_I24


title: Spinal cord, Uninjured, 213s_I21


title: Spinal cord, Injury, P6981_1674


title: Spinal cord, Uninjured, 213s_J14


title: Spinal cord, Uninjured, 213s_I20


title: Spinal cord, Injury, P6981_1673


title: Spinal cord, Injury, P6981_1676


title: Spinal cord, Uninjured, 213s_I11


title: Spinal cord, Uninjured, 213s_I19


title: Spinal cord, Uninjured, 213s_I16


title: Spinal cord, Uninjured, 213s_I13


title: Spinal cord, Injury, P6981_1672


title: Spinal cord, Uninjured, 213s_I10


title: Spinal cord, Injury, P6981_1671


title: Spinal cord, Uninjured, 213s_I09


title: Spinal cord, Uninjured, 213s_I06


title: Spinal cord, Injury, P6981_1667


title: Spinal cord, Injury, P6981_1670


title: Spinal cord, Uninjured, 213s_I05


title: Spinal cord, Injury, P6981_1669


title: Spinal cord, Uninjured, 213s_I04


title: Spinal cord, Uninjured, 213s_H24


title: Spinal cord, Injury, P6981_1665


title: Spinal cord, Injury, P6981_1675


title: Spinal cord, Injury, P6981_1663


title: Spinal cord, Injury, P6981_1664


title: Spinal cord, Uninjured, 213s_H23


title: Spinal cord, Uninjured, 213s_H22


title: Spinal cord, Injury, P6981_1662


title: Spinal cord, Uninjured, 213s_H20


title: Spinal cord, Uninjured, 213s_H18


title: Spinal cord, Injury, P6981_1661


title: Spinal cord, Injury, P6981_1660


title: Spinal cord, Uninjured, 213s_H16


title: Spinal cord, Injury, P6981_1658


title: Spinal cord, Uninjured, 213s_H15


title: Spinal cord, Injury, P6981_1659


title: Spinal cord, Uninjured, 213s_H13


title: Spinal cord, Injury, P6981_1666


title: Spinal cord, Injury, P6981_1668


title: Spinal cord, Injury, P6981_1656


title: Spinal cord, Injury, P6981_1657


title: Spinal cord, Uninjured, 213s_H11


title: Spinal cord, Injury, P6981_1655


title: Spinal cord, Injury, P6981_1654


title: Spinal cord, Uninjured, 213s_H10


title: Spinal cord, Injury, P6981_1653


title: Spinal cord, Uninjured, 213s_H09


title: Spinal cord, Uninjured, 213s_H07


title: Spinal cord, Uninjured, 213s_H06


title: Spinal cord, Injury, P6981_1652


title: Spinal cord, Uninjured, 213s_H02


title: Spinal cord, Injury, P6981_1651


title: Spinal cord, Injury, P6981_1650


title: Spinal cord, Uninjured, 213s_H01


title: Spinal cord, Uninjured, 213s_G23


title: Spinal cord, Injury, P6981_1649


title: Spinal cord, Injury, P6981_1648


title: Spinal cord, Uninjured, 213s_G19


title: Spinal cord, Uninjured, 213s_G16


title: Spinal cord, Injury, P6981_1647


title: Spinal cord, Uninjured, 213s_G17


title: Spinal cord, Injury, P6981_1646


title: Spinal cord, Injury, P6981_1645


title: Spinal cord, Uninjured, 213s_G08


title: Spinal cord, Uninjured, 213s_G13


title: Spinal cord, Uninjured, 213s_G10


title: Spinal cord, Injury, P6981_1644


title: Spinal cord, Injury, P6981_1641


title: Spinal cord, Injury, P6981_1642


title: Spinal cord, Uninjured, 213s_G05


title: Spinal cord, Injury, P6981_1643


title: Spinal cord, Uninjured, 213s_G03


title: Spinal cord, Uninjured, 213s_G01


title: Spinal cord, Injury, P6981_1640


title: Spinal cord, Uninjured, 213s_F24


title: Spinal cord, Injury, P6981_1639


title: Spinal cord, Uninjured, 213s_G04


title: Spinal cord, Injury, P6981_1637


title: Spinal cord, Uninjured, 213s_F19


title: Spinal cord, Injury, P6981_1636


title: Spinal cord, Injury, P6981_1638


title: Spinal cord, Uninjured, 213s_F18


title: Spinal cord, Injury, P6981_1635


title: Spinal cord, Uninjured, 213s_F17


title: Spinal cord, Injury, P6981_1634


title: Spinal cord, Uninjured, 213s_F14


title: Spinal cord, Injury, P6981_1632


title: Spinal cord, Injury, P6981_1633


title: Spinal cord, Uninjured, 213s_F13


title: Spinal cord, Injury, P6981_1631


title: Spinal cord, Uninjured, 213s_G06


title: Spinal cord, Injury, P6981_1629


title: Spinal cord, Uninjured, 213s_F07


title: Spinal cord, Uninjured, 213s_F06


title: Spinal cord, Injury, P6981_1628


title: Spinal cord, Uninjured, 213s_F05


title: Spinal cord, Uninjured, 213s_F03


title: Spinal cord, Injury, P6981_1627


title: Spinal cord, Uninjured, 213s_F10


title: Spinal cord, Uninjured, 213s_F02


title: Spinal cord, Injury, P6981_1625


title: Spinal cord, Injury, P6981_1624


title: Spinal cord, Injury, P6981_1623


title: Spinal cord, Uninjured, 213s_F01


title: Spinal cord, 3d_SCI, 211s_P22


title: Spinal cord, Uninjured, 213s_F16


title: Spinal cord, 3d_SCI, 211s_P21


title: Spinal cord, Injury, P6981_1621


title: Spinal cord, 3d_SCI, 211s_P18


title: Spinal cord, Injury, P6981_1620


title: Spinal cord, Injury, P6981_1630


title: Spinal cord, 3d_SCI, 211s_P16


title: Spinal cord, 3d_SCI, 211s_P17


title: Spinal cord, Injury, P6981_1619


title: Spinal cord, 3d_SCI, 211s_P15


title: Spinal cord, Injury, P6981_1617


title: Spinal cord, 3d_SCI, 211s_P14


title: Spinal cord, Injury, P6981_1616


title: Spinal cord, Injury, P6981_1615


title: Spinal cord, Injury, P6981_1614


title: Spinal cord, 3d_SCI, 211s_P13


title: Spinal cord, 3d_SCI, 211s_P10


title: Spinal cord, Injury, P6981_1626


title: Spinal cord, 3d_SCI, 211s_P09


title: Spinal cord, 3d_SCI, 211s_P11


title: Spinal cord, Injury, P6981_1612


title: Spinal cord, Injury, P6981_1613


title: Spinal cord, 3d_SCI, 211s_P08


title: Spinal cord, 3d_SCI, 211s_P19


title: Spinal cord, 3d_SCI, 211s_P07


title: Spinal cord, Injury, P6981_1611


title: Spinal cord, 3d_SCI, 211s_P06


title: Spinal cord, Injury, P6981_1610


title: Spinal cord, Injury, P6981_1608


title: Spinal cord, Injury, P6981_1622


title: Spinal cord, 3d_SCI, 211s_P05


title: Spinal cord, Injury, P6981_1606


title: Spinal cord, 3d_SCI, 211s_P03


title: Spinal cord, Injury, P6981_1607


title: Spinal cord, Injury, P6981_1605


title: Spinal cord, 3d_SCI, 211s_P02


title: Spinal cord, Injury, P6981_1604


title: Spinal cord, 3d_SCI, 211s_P01


title: Spinal cord, 3d_SCI, 211s_O24


title: Spinal cord, Injury, P6981_1603


title: Spinal cord, Injury, P6981_1601


title: Spinal cord, 3d_SCI, 211s_O23


title: Spinal cord, Injury, P6981_1602


title: Spinal cord, Injury, P6981_1618


title: Spinal cord, Injury, P6981_1600


title: Spinal cord, 3d_SCI, 211s_O22


title: Spinal cord, 3d_SCI, 211s_O21


title: Spinal cord, Injury, P6981_1599


title: Spinal cord, 3d_SCI, 211s_O20


title: Spinal cord, Injury, P6981_1598


title: Spinal cord, 3d_SCI, 211s_O19


title: Spinal cord, 3d_SCI, 211s_O17


title: Spinal cord, Injury, P6981_1609


title: Spinal cord, 3d_SCI, 211s_O18


title: Spinal cord, 3d_SCI, 211s_O16


title: Spinal cord, Injury, P6981_1597


title: Spinal cord, Injury, P6981_1595


title: Spinal cord, 3d_SCI, 211s_P04


title: Spinal cord, Injury, P6981_1596


title: Spinal cord, Injury, P6981_1594


title: Spinal cord, 3d_SCI, 211s_O14


title: Spinal cord, Injury, P6981_1593


title: Spinal cord, Injury, P6981_1592


title: Spinal cord, 3d_SCI, 211s_O10


title: Spinal cord, 3d_SCI, 211s_O12


title: Spinal cord, Injury, P6981_1591


title: Spinal cord, Injury, P6981_1589


title: Spinal cord, Injury, P6981_1587


title: Spinal cord, Injury, P6981_1588


title: Spinal cord, Injury, P6981_1590


title: Spinal cord, 3d_SCI, 211s_O05


title: Spinal cord, 3d_SCI, 211s_O08


title: Spinal cord, 3d_SCI, 211s_O07


title: Spinal cord, 3d_SCI, 211s_O09


title: Spinal cord, Injury, P6981_1586


title: Spinal cord, 3d_SCI, 211s_O01


title: Spinal cord, 3d_SCI, 211s_N21


title: Spinal cord, 3d_SCI, 211s_O04


title: Spinal cord, Injury, P6981_1581


title: Spinal cord, Injury, P6981_1584


title: Spinal cord, 3d_SCI, 211s_N24


title: Spinal cord, Injury, P6981_1583


title: Spinal cord, 3d_SCI, 211s_O15


title: Spinal cord, Injury, P6981_1582


title: Spinal cord, Injury, P6981_1585


title: Spinal cord, 3d_SCI, 211s_O02


title: Spinal cord, 3d_SCI, 211s_O03


title: Spinal cord, Injury, P6981_1577


title: Spinal cord, Injury, P6981_1580


title: Spinal cord, Injury, P6981_1579


title: Spinal cord, 3d_SCI, 211s_N20


title: Spinal cord, 3d_SCI, 211s_N17


title: Spinal cord, Uninjured, P6981_1576


title: Spinal cord, 3d_SCI, 211s_O13


title: Spinal cord, 3d_SCI, 211s_N18


title: Spinal cord, Uninjured, P6981_1574


title: Spinal cord, Uninjured, P6981_1575


title: Spinal cord, 3d_SCI, 211s_N15


title: Spinal cord, Uninjured, P6981_1573


title: Spinal cord, 3d_SCI, 211s_N22


title: Spinal cord, 3d_SCI, 211s_N14


title: Spinal cord, Injury, P6981_1578


title: Spinal cord, 3d_SCI, 211s_N19


title: Spinal cord, Uninjured, P6981_1572


title: Spinal cord, 3d_SCI, 211s_N10


title: Spinal cord, Uninjured, P6981_1570


title: Spinal cord, Uninjured, P6981_1568


title: Spinal cord, Uninjured, P6981_1567


title: Spinal cord, 3d_SCI, 211s_N12


title: Spinal cord, 3d_SCI, 211s_N11


title: Spinal cord, 3d_SCI, 211s_N09


title: Spinal cord, Uninjured, P6981_1566


title: Spinal cord, 3d_SCI, 211s_N16


title: Spinal cord, 3d_SCI, 211s_N08


title: Spinal cord, 3d_SCI, 211s_N06


title: Spinal cord, 3d_SCI, 211s_N04


title: Spinal cord, 3d_SCI, 211s_N07


title: Spinal cord, Uninjured, P6981_1565


title: Spinal cord, 3d_SCI, 211s_N05


title: Spinal cord, 3d_SCI, 211s_N03


title: Spinal cord, Uninjured, P6981_1563


title: Spinal cord, Uninjured, P6981_1564


title: Spinal cord, 3d_SCI, 211s_N02


title: Spinal cord, Injury, P6981_1698


title: Spinal cord, 3d_SCI, 211s_M24


title: Spinal cord, 3d_SCI, 211s_N13


title: Spinal cord, Uninjured, P6981_1560


title: Spinal cord, Uninjured, P6981_1571


title: Spinal cord, Uninjured, P6981_1559


title: Spinal cord, Uninjured, P6981_1569


title: Spinal cord, 3d_SCI, 211s_M23


title: Spinal cord, Uninjured, P6981_1562


title: Spinal cord, 3d_SCI, 211s_M19


title: Spinal cord, 3d_SCI, 211s_M18


title: Spinal cord, 3d_SCI, 211s_M22


title: Spinal cord, 3d_SCI, 211s_M20


title: Spinal cord, Uninjured, P6981_1561


title: Spinal cord, 3d_SCI, 211s_M17


title: Spinal cord, Uninjured, P6981_1556


title: Spinal cord, 3d_SCI, 211s_M21


title: Spinal cord, Uninjured, P6981_1554


title: Spinal cord, Uninjured, P6981_1555


title: Spinal cord, Uninjured, P6981_1557


title: Spinal cord, Uninjured, P6981_1553


title: Spinal cord, 3d_SCI, 211s_M13


title: Spinal cord, Uninjured, P6981_1550


title: Spinal cord, 3d_SCI, 211s_M14


title: Spinal cord, 3d_SCI, 211s_M16


title: Spinal cord, Uninjured, P6981_1551


title: Spinal cord, Uninjured, P6981_1548


title: Spinal cord, Uninjured, P6981_1558


title: Spinal cord, 3d_SCI, 211s_M12


title: Spinal cord, Uninjured, P6981_1546


title: Spinal cord, Uninjured, P6981_1547


title: Spinal cord, 3d_SCI, 211s_M11


title: Spinal cord, 3d_SCI, 211s_M10


title: Spinal cord, Uninjured, P6981_1545


title: Spinal cord, 3d_SCI, 211s_M09


title: Spinal cord, Uninjured, P6981_1552


title: Spinal cord, Uninjured, P6981_1544


title: Spinal cord, Uninjured, P6981_1549


title: Spinal cord, Uninjured, P6981_1543


title: Spinal cord, 3d_SCI, 211s_M06


title: Spinal cord, 3d_SCI, 211s_M08


title: Spinal cord, Uninjured, P6981_1542


title: Spinal cord, 3d_SCI, 211s_M04


title: Spinal cord, 3d_SCI, 211s_M05


title: Spinal cord, 3d_SCI, 211s_M03


title: Spinal cord, 3d_SCI, 211s_M07


title: Spinal cord, Uninjured, P6981_1539


title: Spinal cord, 3d_SCI, 211s_M02


title: Spinal cord, Uninjured, P6981_1540


title: Spinal cord, Uninjured, P6981_1536


title: Spinal cord, 3d_SCI, 211s_L24


title: Spinal cord, 3d_SCI, 211s_M01


title: Spinal cord, 3d_SCI, 211s_M15


title: Spinal cord, 3d_SCI, 211s_L23


title: Spinal cord, Uninjured, P6981_1534


title: Spinal cord, Uninjured, P6981_1535


title: Spinal cord, 3d_SCI, 211s_L21


title: Spinal cord, Uninjured, P6981_1533


title: Spinal cord, Uninjured, P6981_1531


title: Spinal cord, 3d_SCI, 211s_L18


title: Spinal cord, 3d_SCI, 211s_L17


title: Spinal cord, Uninjured, P6981_1532


title: Spinal cord, 3d_SCI, 211s_L15


title: Spinal cord, Uninjured, P6981_1530


title: Spinal cord, Uninjured, P6981_1541


title: Spinal cord, Uninjured, P6981_1538


title: Spinal cord, Uninjured, P6981_1529


title: Spinal cord, Uninjured, P6981_1537


title: Spinal cord, 3d_SCI, 211s_L09


title: Spinal cord, 3d_SCI, 211s_L12


title: Spinal cord, 3d_SCI, 211s_L14


title: Spinal cord, 3d_SCI, 211s_L10


title: Spinal cord, 3d_SCI, 211s_L13


title: Spinal cord, Uninjured, P6981_1524


title: Spinal cord, Uninjured, P6981_1527


title: Spinal cord, Uninjured, P6981_1528


title: Spinal cord, Uninjured, P6981_1526


title: Spinal cord, Uninjured, P6981_1525


title: Spinal cord, 3d_SCI, 211s_L02


title: Spinal cord, 3d_SCI, 211s_L06


title: Spinal cord, Uninjured, P6981_1523


title: Spinal cord, 3d_SCI, 211s_L01


title: Spinal cord, 3d_SCI, 211s_K21


title: Spinal cord, Uninjured, P6981_1521


title: Spinal cord, 3d_SCI, 211s_K19


title: Spinal cord, Uninjured, P6981_1522


title: Spinal cord, Uninjured, P6981_1520


title: Spinal cord, 3d_SCI, 211s_K17


title: Spinal cord, 3d_SCI, 211s_K16


title: Spinal cord, Uninjured, P6981_1518


title: Spinal cord, Uninjured, P6981_1519


title: Spinal cord, Uninjured, P6981_1517


title: Spinal cord, Uninjured, P6981_1516


title: Spinal cord, 3d_SCI, 211s_K15


title: Spinal cord, 3d_SCI, 211s_K10


title: Spinal cord, Uninjured, P6981_1515


title: Spinal cord, 3d_SCI, 211s_K09


title: Spinal cord, Uninjured, P6981_1514


title: Spinal cord, 3d_SCI, 211s_L04


title: Spinal cord, Uninjured, P6981_1512


title: Spinal cord, 3d_SCI, 211s_K03


title: Spinal cord, Uninjured, P6981_1510


title: Spinal cord, 3d_SCI, 211s_K06


title: Spinal cord, Uninjured, P6981_1509


title: Spinal cord, 3d_SCI, 211s_K02


title: Spinal cord, Uninjured, P6981_1513


title: Spinal cord, 3d_SCI, 211s_K07


title: Spinal cord, 3d_SCI, 211s_K01


title: Spinal cord, Uninjured, P6981_1508


title: Spinal cord, Uninjured, P6981_1507


title: Spinal cord, Uninjured, P6981_1511


title: Spinal cord, 3d_SCI, 211s_J24


title: Spinal cord, Uninjured, P6981_1506


title: Spinal cord, 3d_SCI, 211s_J22


title: Spinal cord, Uninjured, P6981_1505


title: Spinal cord, Uninjured, P6981_1504


title: Spinal cord, 3d_SCI, 211s_J21


title: Spinal cord, 3d_SCI, 211s_J18


title: Spinal cord, Uninjured, P6981_1503


title: Spinal cord, 3d_SCI, 211s_J17


title: Spinal cord, 3d_SCI, 211s_J16


title: Spinal cord, Uninjured, P6981_1501


title: Spinal cord, 3d_SCI, 211s_J15


title: Spinal cord, Uninjured, P6981_1500


title: Spinal cord, Uninjured, P6981_1502


title: Spinal cord, Uninjured, P6981_1499


title: Spinal cord, 3d_SCI, 211s_K05


title: Spinal cord, 3d_SCI, 211s_J11


title: Spinal cord, 3d_SCI, 211s_J06


title: Spinal cord, 3d_SCI, 211s_J12


title: Spinal cord, 3d_SCI, 211s_J02


title: Spinal cord, 3d_SCI, 211s_J01


title: Spinal cord, Uninjured, P6981_1496


title: Spinal cord, Uninjured, P6981_1498


title: Spinal cord, Uninjured, P6981_1497


title: Spinal cord, Uninjured, P6981_1493


title: Spinal cord, 3d_SCI, 211s_J23


title: Spinal cord, Uninjured, P6981_1495


title: Spinal cord, 3d_SCI, 211s_I24


title: Spinal cord, 3d_SCI, 211s_I22


title: Spinal cord, 3d_SCI, 211s_I23


title: Spinal cord, Uninjured, P6981_1494


title: Spinal cord, Uninjured, P6981_1490


title: Spinal cord, 3d_SCI, 211s_I20


title: Spinal cord, Uninjured, P6981_1489


title: Spinal cord, Uninjured, P6981_1492


title: Spinal cord, 3d_SCI, 211s_I19


title: Spinal cord, 3d_SCI, 211s_I18


title: Spinal cord, Uninjured, P6981_1491


title: Spinal cord, Uninjured, P6981_1488


title: Spinal cord, Uninjured, P6981_1487


title: Spinal cord, 3d_SCI, 211s_I16


title: Spinal cord, Uninjured, P6981_1486


title: Spinal cord, 3d_SCI, 211s_I17


title: Spinal cord, 3d_SCI, 211s_I14


title: Spinal cord, Uninjured, P6981_1485


title: Spinal cord, 3d_SCI, 211s_I13


title: Spinal cord, Uninjured, P6981_1484


title: Spinal cord, 3d_SCI, 211s_I21


title: Spinal cord, 3d_SCI, 211s_I05


title: Spinal cord, Uninjured, P6981_1482


title: Spinal cord, 3d_SCI, 211s_I06


title: Spinal cord, Uninjured, P6981_1483


title: Spinal cord, Uninjured, P6981_1481


title: Spinal cord, 3d_SCI, 211s_I03


title: Spinal cord, 3d_SCI, 211s_I11


title: Spinal cord, Uninjured, P6981_1480


title: Spinal cord, Uninjured, 209s_P21


title: Spinal cord, Uninjured, P6981_1479


title: Spinal cord, Uninjured, P6981_1478


title: Spinal cord, Uninjured, P6981_1477


title: Spinal cord, Uninjured, P6981_1476


title: Spinal cord, Uninjured, 209s_P20


title: Spinal cord, Uninjured, 209s_P19


title: Spinal cord, Uninjured, P6981_1475


title: Spinal cord, Uninjured, P6981_1474


title: Spinal cord, 3d_SCI, 211s_I01


title: Spinal cord, Uninjured, 209s_P13


title: Spinal cord, Uninjured, 209s_P16


title: Spinal cord, Uninjured, P6981_1473


title: Spinal cord, Uninjured, 209s_P06


title: Spinal cord, Uninjured, P6981_1472


title: Spinal cord, Uninjured, 209s_P10


title: Spinal cord, Uninjured, P6981_1471


title: Spinal cord, Uninjured, P6981_1470


title: Spinal cord, Uninjured, 209s_P11


title: Spinal cord, Uninjured, P6981_1469


title: Spinal cord, Uninjured, P6981_1468


title: Spinal cord, Uninjured, P6981_1467


title: Spinal cord, Uninjured, 209s_P03


title: Spinal cord, Uninjured, 209s_P01


title: Spinal cord, Uninjured, P6981_1466


title: Spinal cord, Uninjured, 209s_O24


title: Spinal cord, Uninjured, P6981_1465


title: Spinal cord, Uninjured, 209s_P04


title: Spinal cord, 3d_SCI, 211s_I04


title: Spinal cord, Uninjured, 209s_O20


title: Spinal cord, Uninjured, 209s_O19


title: Spinal cord, Uninjured, P6981_1462


title: Spinal cord, Uninjured, 209s_O18


title: Spinal cord, Uninjured, P6981_1461


title: Spinal cord, Uninjured, P6981_1460


title: Spinal cord, Uninjured, P6981_1463


title: Spinal cord, Uninjured, 209s_O17


title: Spinal cord, Uninjured, P6981_1459


title: Spinal cord, Uninjured, 209s_O15


title: Spinal cord, Uninjured, 209s_P05


title: Spinal cord, Uninjured, 209s_O14


title: Spinal cord, Uninjured, 209s_O11


title: Spinal cord, Uninjured, P6981_1457


title: Spinal cord, Uninjured, P6981_1458


title: Spinal cord, Uninjured, P6981_1456


title: Spinal cord, Uninjured, 209s_O10


title: Spinal cord, Uninjured, 209s_O13


title: Spinal cord, Uninjured, P6981_1454


title: Spinal cord, Uninjured, P6981_1453


title: Spinal cord, Uninjured, 209s_O04


title: Spinal cord, Uninjured, P6981_1455


title: Spinal cord, Uninjured, P6981_1452


title: Spinal cord, Uninjured, P6981_1464


title: Spinal cord, Uninjured, 209s_O06


title: Spinal cord, Uninjured, 209s_O21


title: Spinal cord, Uninjured, 209s_O01


title: Spinal cord, Uninjured, 209s_N22


title: Spinal cord, Uninjured, P6981_1450


title: Spinal cord, Uninjured, P6981_1449


title: Spinal cord, Uninjured, 209s_N19


title: Spinal cord, Uninjured, 209s_N14


title: Spinal cord, Uninjured, 209s_N16


title: Spinal cord, Uninjured, P6981_1447


title: Spinal cord, Uninjured, P6981_1448


title: Spinal cord, Uninjured, 209s_N13


title: Spinal cord, Uninjured, 209s_N12


title: Spinal cord, Uninjured, P6981_1445


title: Spinal cord, Uninjured, P6981_1446


title: Spinal cord, Uninjured, 209s_N11


title: Spinal cord, Uninjured, P6981_1444


title: Spinal cord, Uninjured, 209s_O08


title: Spinal cord, Uninjured, 209s_N09


title: Spinal cord, Uninjured, P6981_1442


title: Spinal cord, Uninjured, 209s_N07


title: Spinal cord, Uninjured, 209s_N08


title: Spinal cord, Uninjured, P6981_1443


title: Spinal cord, Uninjured, P6981_1441


title: Spinal cord, Uninjured, P6981_1451


title: Spinal cord, Uninjured, P6981_1439


title: Spinal cord, Uninjured, 209s_N05


title: Spinal cord, Uninjured, 209s_M24


title: Spinal cord, Uninjured, 209s_M23


title: Spinal cord, Uninjured, P6981_1438


title: Spinal cord, Uninjured, P6981_1437


title: Spinal cord, Uninjured, P6981_1435


title: Spinal cord, Uninjured, 209s_M20


title: Spinal cord, Uninjured, P6981_1433


title: Spinal cord, Uninjured, 209s_M22


title: Spinal cord, Uninjured, 209s_M17


title: Spinal cord, Uninjured, P6981_1436


title: Spinal cord, Uninjured, 209s_M21


title: Spinal cord, Uninjured, 209s_M14


title: Spinal cord, Uninjured, P6981_1432


title: Spinal cord, Uninjured, 209s_M13


title: Spinal cord, Uninjured, 209s_M09


title: Spinal cord, Uninjured, P6981_1431


title: Spinal cord, Uninjured, P6981_1429


title: Spinal cord, Uninjured, 209s_M08


title: Spinal cord, Uninjured, P6981_1430


title: Spinal cord, Uninjured, 209s_M07


title: Spinal cord, Uninjured, P6981_1440


title: Spinal cord, Uninjured, P6981_1428


title: Spinal cord, Uninjured, 209s_M06


title: Spinal cord, Uninjured, P6981_1427


title: Spinal cord, Uninjured, P6981_1425


title: Spinal cord, Uninjured, P6981_1426


title: Spinal cord, Uninjured, 209s_N06


title: Spinal cord, Uninjured, P6981_1424


title: Spinal cord, Uninjured, 209s_L24


title: Spinal cord, Uninjured, P6981_1423


title: Spinal cord, Uninjured, 209s_M02


title: Spinal cord, Uninjured, P6981_1422


title: Spinal cord, Uninjured, P6981_1420


title: Spinal cord, Uninjured, 209s_L17


title: Spinal cord, Uninjured, P6981_1421


title: Spinal cord, Uninjured, P6981_1434


title: Spinal cord, Uninjured, 209s_L12


title: Spinal cord, Uninjured, P6981_1419


title: Spinal cord, Uninjured, 209s_L05


title: Spinal cord, Uninjured, P6981_1417


title: Spinal cord, Uninjured, P6981_1418


title: Spinal cord, Uninjured, 209s_L04


title: Spinal cord, Uninjured, P6981_1416


title: Spinal cord, Uninjured, 209s_M04


title: Spinal cord, Uninjured, 209s_M03


title: Spinal cord, Uninjured, P6981_1415


title: Spinal cord, Uninjured, P6981_1412


title: Spinal cord, Uninjured, 209s_L03


title: Spinal cord, Uninjured, 209s_K22


title: Spinal cord, Uninjured, P6981_1413


title: Spinal cord, Uninjured, 209s_L02


title: Spinal cord, Uninjured, P6981_1414


title: Spinal cord, Uninjured, P6981_1410


title: Spinal cord, Uninjured, 209s_K20


title: Spinal cord, Uninjured, 209s_K19


title: Spinal cord, Uninjured, 209s_L18


title: Spinal cord, Uninjured, 209s_K24


title: Spinal cord, Uninjured, P6981_1411


title: Spinal cord, Uninjured, 209s_L14


title: Spinal cord, Uninjured, P6981_1409


title: Spinal cord, Uninjured, 209s_L13


title: Spinal cord, Uninjured, 209s_K15


title: Spinal cord, Uninjured, 209s_L10


title: Spinal cord, Uninjured, P6981_1407


title: Spinal cord, Uninjured, P6981_1405


title: Spinal cord, Uninjured, 209s_K12


title: Spinal cord, Uninjured, 209s_K09


title: Spinal cord, Uninjured, P6981_1404


title: Spinal cord, Uninjured, 209s_K10


title: Spinal cord, Uninjured, P6981_1403


title: Spinal cord, Uninjured, 209s_K04


title: Spinal cord, Uninjured, P6981_1402


title: Spinal cord, Uninjured, 209s_J23


title: Spinal cord, Uninjured, P6981_1400


title: Spinal cord, Uninjured, P6981_1401


title: Spinal cord, Uninjured, 209s_K01


title: Spinal cord, Uninjured, P6981_1399


title: Spinal cord, Uninjured, P6981_1398


title: Spinal cord, Uninjured, 209s_J20


title: Spinal cord, Uninjured, 209s_J21


title: Spinal cord, Uninjured, P6981_1397


title: Spinal cord, Uninjured, 209s_J19


title: Spinal cord, Uninjured, P6981_1396


title: Spinal cord, Uninjured, 209s_K17


title: Spinal cord, Uninjured, P6981_1408


title: Spinal cord, Uninjured, 209s_J18


title: Spinal cord, Uninjured, 209s_K14


title: Spinal cord, Uninjured, P6981_1394


title: Spinal cord, Uninjured, 209s_J13


title: Spinal cord, Uninjured, 209s_J12


title: Spinal cord, Uninjured, P6981_1406


title: Spinal cord, Uninjured, P6981_1392


title: Spinal cord, Uninjured, P6981_1391


title: Spinal cord, Uninjured, 209s_J09


title: Spinal cord, Uninjured, 209s_J10


title: Spinal cord, Uninjured, P6981_1390


title: Spinal cord, Uninjured, 209s_J22


title: Spinal cord, Uninjured, P6981_1389


title: Spinal cord, Uninjured, 209s_J06


title: Spinal cord, Uninjured, 209s_J04


title: Spinal cord, Uninjured, 209s_J02


title: Spinal cord, Uninjured, 209s_I21


title: Spinal cord, Uninjured, P6981_1387


title: Spinal cord, Uninjured, P6981_1388


title: Spinal cord, Uninjured, P6981_1385


title: Spinal cord, Uninjured, 209s_I15


title: Spinal cord, Uninjured, 209s_I18


title: Spinal cord, Uninjured, 209s_I14


title: Spinal cord, Uninjured, P6981_1395


title: Spinal cord, Uninjured, 209s_I10


title: Spinal cord, Uninjured, P6981_1384


title: Spinal cord, Uninjured, P6981_1393


title: Spinal cord, Uninjured, P6981_1382


title: Spinal cord, Uninjured, P6981_1383


title: Spinal cord, Uninjured, 209s_I09


title: Spinal cord, Uninjured, 209s_I07


title: Spinal cord, Uninjured, P6981_1380


title: Spinal cord, Uninjured, P6981_1381


title: Spinal cord, Uninjured, 209s_J11


title: Spinal cord, Uninjured, 209s_I06


title: Spinal cord, Uninjured, 209s_I04


title: Spinal cord, Uninjured, P6981_1378


title: Spinal cord, Uninjured, P6981_1377


title: Spinal cord, Uninjured, 209s_H22


title: Spinal cord, Uninjured, P6981_1386


title: Spinal cord, Uninjured, 209s_H21


title: Spinal cord, Uninjured, P6981_1375


title: Spinal cord, Uninjured, 209s_H18


title: Spinal cord, Uninjured, 209s_H16


title: Spinal cord, Uninjured, P6981_1373


title: Spinal cord, Uninjured, P6981_1372


title: Spinal cord, Uninjured, 209s_H15


title: Spinal cord, Uninjured, P6981_1370


title: Spinal cord, Uninjured, 209s_H14


title: Spinal cord, Uninjured, P6981_1371


title: Spinal cord, Uninjured, 209s_H19


title: Spinal cord, Uninjured, 209s_H07


title: Spinal cord, Uninjured, 209s_H04


title: Spinal cord, Uninjured, 209s_H01


title: Spinal cord, Uninjured, P6981_1369


title: Spinal cord, Uninjured, 209s_G20


title: Spinal cord, Uninjured, P6981_1367


title: Spinal cord, Uninjured, P6981_1368


title: Spinal cord, Uninjured, P6981_1366


title: Spinal cord, Uninjured, 209s_G15


title: Spinal cord, Uninjured, P6981_1365


title: Spinal cord, Uninjured, P6981_1379


title: Spinal cord, Uninjured, 209s_H24


title: Spinal cord, Uninjured, P6981_1364


title: Spinal cord, Uninjured, P6981_1376


title: Spinal cord, Uninjured, 209s_G12


title: Spinal cord, Uninjured, P6981_1363


title: Spinal cord, Uninjured, P6981_1374


title: Spinal cord, Uninjured, 209s_G10


title: Spinal cord, Uninjured, P6981_1362


title: Spinal cord, Uninjured, 209s_G07


title: Spinal cord, Uninjured, 209s_G04


title: Spinal cord, Uninjured, P6981_1361


title: Spinal cord, Uninjured, 209s_G03


title: Spinal cord, Uninjured, P6981_1360


title: Spinal cord, Uninjured, P6981_1359


title: Spinal cord, Uninjured, 209s_F23


title: Spinal cord, Uninjured, P6981_1357


title: Spinal cord, Uninjured, P6981_1358


title: Spinal cord, Uninjured, 209s_F22


title: Spinal cord, Uninjured, 209s_F21


title: Spinal cord, Uninjured, P6981_1356


title: Spinal cord, Uninjured, 209s_F16


title: Spinal cord, Uninjured, 209s_F15


title: Spinal cord, Uninjured, P6981_1354


title: Spinal cord, Uninjured, P6981_1355


title: Spinal cord, Uninjured, 209s_G13


title: Spinal cord, Uninjured, P6981_1353


title: Spinal cord, Uninjured, 209s_F14


title: Spinal cord, Uninjured, 209s_F17


title: Spinal cord, Uninjured, P6981_1351


title: Spinal cord, Uninjured, 209s_F08


title: Spinal cord, Uninjured, P6981_1352


title: Spinal cord, Uninjured, P6981_1350


title: Spinal cord, Uninjured, 209s_F11


title: Spinal cord, Uninjured, 209s_F03


title: Spinal cord, Uninjured, P6981_1349


title: Spinal cord, Uninjured, 209s_F01


title: Spinal cord, Uninjured, P6981_1348


title: Spinal cord, Uninjured, P6981_1347


title: Spinal cord, Uninjured, P6981_1346


title: 806

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

data_processing:
Raw files were processed with Cell Ranger Count v3.0.2.
Outputs for each samples are provided in filtered_feature_bc_matrices.tar.gz files.
Assembly: mm10

source_name: brain

extract_protocol:
For single nuclei dissociation, a protocol from previous study was followed [108]. Briefly, frozen tissue punches were chopped and transferred to 450ul of chilled (4°C) homogenization buffer (250mM sucrose, 25mM KCL, 5mM MgCl2, 10mM Tris buffer (pH 8.0), 1μM DTT, 1x protease inhibitor, RNaseIn 0.4 U/ul, Superasin 0.2 U/ul, 0.1% Triton X-100). After the Dounce homogenization and filtering (40μm), the nuclei were concentrated by centrifugation (1,000g for 8 min at 4°C). For staining, anti-NeuN antibody, Hoeshst, and Alexa 488 secondary antibody were treated and incubated on rocker in cold room for 30 min. The nuclei were resuspended in 600 ul FACS buffer (1% unacetylated BSA, RNaseIn 0.4 U/ul, PBS) for FACS to further purify the nuclei for sequencing. The nuclei were first sorted based on Hoechst signal and then based on Alexa 488 fluorophore, collecting 50,000 nuclei per mouse.
Libraries were constructed using the 3’ Expression-Single-Cell RNA-Seq using 10X Chromium System (v3.1), according to the manufacturer’s instructions. The nuclei were brought to a concentration of 500 nuclei/μl and 5,000 nuclei were loaded to prepare libraries. Libraries were then sequenced (pair-end sequencing) on the Illumina NovaSeq6000 at the Iowa Institute of Human Genetics at University of Iowa. The depth of sequencing per flow cell was 50,000 reads per nuclei.

value: brain

value: Female

tag: condition


title: 807


title: Spinal cord, Uninjured, P6981_1344

value: Spinal cord


title: 811


title: 803

value: wild-type


title: Spinal cord, Uninjured, P6981_1343

value: Perivascular cells


title: Spinal cord, Uninjured, P6981_1342

value: EGFP+; tdTomato-


title: 796


title: 798


title: Spinal cord, Uninjured, P6981_1341


title: Spinal cord, Uninjured, P6981_1340


title: Spinal cord, Uninjured, P6981_1338


title: 795


title: Skin, TRPV1 activation,  B6 RNA

city: SAN FRANCISCO

first: Konrad

last: Knopper

state: CA

address: 513 Parnassus Ave

institute: UCSF

description: 210803_A00269_0538_BH3WY7DSX2_cysterj-WT_GEX_dual_index

data_processing:
CellRanger v6.1 aggr and count function was used to aggregate reads across lanes and libraries into CellRanger output files.
Downstream analysis and Hashtag asignment was done using R and Python.
Assembly: mm10
Supplementary files format and content: h5

source_name: Backskin

growth_protocol: Animals were housed in a pathogen-free environment in the Laboratory Animal Resource Center at the University of California, San Francisco

extract_protocol:
Back skin from TRPV1hM3Dq and control mice (three mice per group) treated daily with a CNO intradermal injection for three consecutive days, were dissected, separated into the subcutis and dermal-epidermal fractions and then digested. The dermal-epidermal and subcutis fractions were stained separately with TotalSeq™ anti-mouse Hashtag antibodies to mark the cells’ anatomical location. Thy1+ SCA1+ stromal cells (CD45−CD31− EpCAM−) were sorted. The dermal-epidermal and subcutis fractions from TRPV1 activated and control samples were pooled together and sorted using a BD FACSAriaII with a 100-μm nozzle into RPMI medium supplemented with 10% FBS.
Single cells were quantified using a hemocytometer. Cell capture, cDNA library preparation, quality control, and sequencing was performed at UC Irvine Genomic High Throughput Facility. SingleCell 3'- 10x

treatment_protocol: 7 weeks old TRPV1hM3Dq expressing mice and their controls (DREADD negative) were anesthetized with isoflurane and an area of 2x2cm of dorsal hair was shortened with clippers. A total of 150ul of CNO (diluted 1.3ug/ml in PBS) was injected intradermally in the shaved patch of skin, with about 6 injection points of 25ul each which were evenly spaced in the shaved area. This was repeated daily for three consecutive days.

value: Backskin

value: N/A. Primary cells were used in this study.

value: Lin- Thy1+ SCA1+

value: x3 daily CNO intradermal injections

tag: library type

value: mRNA


title: Spinal cord, Uninjured, P6981_1339


title: Spinal cord, Uninjured, P6981_1337


title: Skin, TRPV1 activation,  Chrm RNA

description: 210803_A00269_0538_BH3WY7DSX2_cysterj-CHRM3_GEX_dual_index


title: Skin, TRPV1 activation,  B6 HTO

tag: hto

value: HTO


title: Skin, TRPV1 activation,  CD45+, B6 RNA

description:
cysterj-WT_GEX
cysterj-WT_GEX

data_processing:
CellRanger v7 aggr and count function was used to aggregate reads across lanes and libraries into CellRanger output files.
Downstream analysis and Hashtag asignment was done using Seurat.
Assembly: mm10
Supplementary files format and content: h5

extract_protocol:
Back skin from TRPV1hM3Dq and control mice (three mice per group) 3.5 hours after a single CNO intradermal injection, were dissected, subcutis was removed mechanically and the dermal-epidermal fractions were digested. TotalSeq™ anti-mouse Hashtag antibodies were used to mark the different mice before pooling all control and TRPV1 activated samples together for staining and sorting. CD45+ were sorted. The dermal-epidermal and subcutis fractions from TRPV1 activated and control samples were pooled together and sorted using a BD FACSAriaII with a 100-μm nozzle into RPMI medium supplemented with 10% FBS.
Single cells were quantified using a hemocytometer. Cell capture, cDNA library preparation, quality control, and sequencing was performed at UC Irvine Genomic High Throughput Facility. SingleCell 3'- 10x

treatment_protocol: 7 weeks old TRPV1hM3Dq expressing mice and their controls (DREADD negative) were anesthetized with isoflurane and an area of 2x2cm of dorsal hair was shortened with clippers. A total of 150ul of CNO (diluted 1.3ug/ml in PBS) was injected intradermally in the shaved patch of skin, with about 6 injection points of 25ul each which were evenly spaced in the shaved area.

value: 3.5 hours after an intradermal CNO injection


title: Spinal cord, Injury , P6981_1336

value: female


title: Skin, TRPV1 activation,  Chrm HTO

description: 210803_A00269_0538_BH3WY7DSX2_cysterj-CHRM3_FB-CSP_Dual_Index


title: Skin, TRPV1 activation,  CD45+, Chrm RNA

description:
cysterj-CHRM_GEX
cysterj-CHRM_GEX


title: Spinal cord, Injury , P6981_1333


title: Spinal cord, Injury , P6981_1334


title: Spinal cord, Injury , P6981_1335


title: Skin, TRPV1 activation,  CD45+, B6 HTO

description:
cysterj-WT_FB-CSP
cysterj-WT_FB-CSP


title: 809

value: male


title: Spinal cord, Uninjured, P6981_1345


title: Skin, TRPV1 activation,  CD45+, Chrm HTO

description:
cysterj-CHRM_FB-CSP
cysterj-CHRM_FB-CSP


title: Spinal cord, Injury , P6981_1332

value: EGFP+; tdTomato+


title: C57BL/6J, Aged mouse4, RPE/choroid, 20-24 months

city: Johnson City

first: Mark

middle: Ellsworth

last: Kleinman

state: Tennessee

address: Quillen College of Medicine

department: Department of Surgery

institute: East Tennessee State University

data_processing:
Paired-end 150 bp raw reads were trimmed to eliminate Truseq adapters and bases from the 3’ end with quality scores less than 20 using cutadapt (ver 4.4). Trimmed reads were aligned to the Mus musculus (house mouse) genome assembly GRCm39 (mm39) from Genome Reference Consortium [GCA_000001635.9 GCF_000001635.27] using STAR [44].
The expression level of ENSEMBL genes was quantified using FeatureCounts. Differential expression statistics were computed using edgeR, using raw expression counts.
Assembly: GRCm39 (mm39)
Supplementary files format and content: edgeR results for all the samples
Supplementary files format and content: normalized TPM counts

source_name: RPE/choroid

growth_protocol: The mice were purchased from the Jackson Laboratory and housed under standard conditions (23±1°C, 40%–50% humidity, and ad libitum access to food and water).

extract_protocol:
All mice were humanely euthanized by administering CO2 gas followed by cervical dislocation. The eyes were immediately enucleated to collect the neural retina and RPE/choroid tissues. The isolated eyes were placed in the cold petri dish under a surgical microscope. With careful precision, the anterior parts, including the cornea, lens, and iris, as well as connective tissues, muscles, and optic nerve, were excised. Radial cuts were made symmetrically in a four-leaf pattern, allowing for the careful removal of the neural retina from the mouse eyecup. The pigmented RPE/choroid layer was gently scraped from the sclera. RPE/choroid and neural retina tissues were immediately transferred to TRIzol reagent (Invitrogen 15596026, Carlsbad, CA). Subsequently, RNA purification and on-column genomic DNA digestion were conducted using the Pure Link RNA Micro Kit (Invitrogen 12183016, Carlsbad, CA).
Ribosomal RNAs were removed with the Qiagen FastSelect -rRNA HMR Kit (Human/Mouse/Rat). RNA libraries were constructed using NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (Perkin Elmer, Waltham, MA) as per manufacturer's instructions.

value: RPE/choroid

tag: age

value: 22-24 months


title: Spinal cord, Injury , P6981_1331


title: C57BL/6J, Aged mouse3, RPE/choroid, 20-24 months

value: Female


title: Spinal cord, Injury , P6981_1330

value: Spinal cord


title: Spinal cord, Injury , P6981_1329


title: C57BL/6J, Aged mouse2, RPE/choroid, 20-24 months

value: Male


title: Spinal cord, Injury , P6981_1328

value: Perivascular cells


title: Spinal cord, Injury , P6981_1327


title: C57BL/6J, Young mouse4, RPE/choroid, 2-3 months

value: 2-3 months


title: Spinal cord, Injury , P6981_1324


title: Spinal cord, Injury , P6981_1326


title: C57BL/6J, Young mouse2, RPE/choroid, 2-3 months


title: VSMC, NR4A3KO, Day1,rep2

first: Wenqi

last: Ma

state: Shanghai

address: 227 Chongqing South Road, Huangpu District, Shanghai, China

data_processing:
To select complementary DNA fragments of preferentially 250 to 300 base pairs (bp) in length, the library fragments were purified with an AMPure XP system
USER Enzyme (NEB) was used with size-selected fragments and polymerase chain reaction (PCR) products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system
The clustering of the index-coded samples was performed on the cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions
After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes counts for each sample
Supplementary files format and content: tab-delimited text file include RPKM values for each sample

source_name: Aorta

growth_protocol: Cells were cultured in DMEM/F12 medium containing 10 % fetal bovine serum (FBS) and 1 % penicillin-streptomycin, and 10 mM β-GP.

extract_protocol:
Total RNA was extracted from the cultured cell samples using TRIzol Reagent. RNA quality and quantity were measured using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations, and index codes were Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells at approximately 80 % confluence were cultured in DMEM/F12 medium containing 10 % fetal bovine serum (FBS) and 1 % penicillin-streptomycin, and 10 mM β-GP.

value: Aorta

value: VSMC

value: Primary

value: β-GP


title: Spinal cord, Injury , P6981_1325


title: Spinal cord, Injury , P6981_1323


title: C57BL/6J, Young mouse3, RPE/choroid, 2-3 months


title: C57BL/6J, Young mouse1, RPE/choroid, 2-3 months


title: VSMC, NR4A3KO, Day1,rep3


title: Spinal cord, Injury , P6981_1321


title: Spinal cord, Injury , P6981_1322


title: VSMC, NR4A3KO, Day1,rep1


title: VSMC, WT, Day1,rep2

value: WT


title: VSMC, WT, Day1,rep1


title: Spinal cord, Injury , P6981_1319


title: Spinal cord, Injury , P6981_1320


title: VSMC, WT, Day1,rep3


title: C57BL/6J, Aged mouse1, RPE/choroid, 20-24 months


title: VSMC, NR4A3KO, Day14,rep3


title: Spinal cord, Injury , P6981_1317


title: Spinal cord, Injury , P6981_1318


title: Spinal cord, Injury , P6981_1315


title: VSMC, NR4A3KO, Day14,rep2


title: Spinal cord, Injury , P6981_1316


title: VSMC, WT, Day14,rep3


title: Spinal cord, Injury , P6981_1314


title: VSMC, WT, Day14,rep2


title: VSMC, NR4A3KO, Day14,rep1


title: Spinal cord, Injury , P6981_1313


title: VSMC, WT, Day14,rep1


title: Spinal cord, Injury , P6981_1312


title: VSMC, WT, NR4A3 CUT&Tag, REP2

data_processing:
*library strategy: CUT&Tag
All reads produced by CUT&Tag of NR4A3 and H3K18la were aligned to the Mouse reference genome (UCSC, mm10 assembly) using Bowtie2 with options: –local– very-sensitive-local–no-unal–no-mixed–no-discordant–phred33 -I 10 -X 700.
Sequence tags were aligned to the genome and then subsequently analyzed by MACS2 (version 2.2.7.1) to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that we considered to be putative binding sites.
We considered differential peaks with FDR lower than 5 % as statistically significant.
Visualization of peak distribution along genomic regions of interested genes was performed with IGV.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes counts for each sample
Supplementary files format and content: bigwig, narrowpeak

extract_protocol:
Total RNA was extracted from the cultured cell samples using TRIzol Reagent. RNA quality and quantity were measured using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
Libraries were sequenced on Illumina Nova-PE150, and 150-bp paired-end reads were generated

value: VCMC


title: VSMC, NR4A3KO, NR4A3 CUT&Tag


title: VSMC, WT, NR4A3 Input


title: Spinal cord, Injury , P6981_1311


title: Spinal cord, Injury , P6981_1308


title: VSMC, WT, NR4A3 CUT&Tag, REP1


title: Spinal cord, Injury , P6981_1309


title: Spinal cord, Injury , P6981_1307


title: VSMC, NR4A3KO, H3K18LA Input


title: Spinal cord, Injury , P6981_1305


title: VSMC, WT, H3K18LA Input


title: Spinal cord, Injury , P6981_1304


title: Spinal cord, Injury , P6981_1306


title: Spinal cord, Injury , P6981_1303